Nov 17 11:05:39.002 INFO testing TuBieJun/consensus against master#6b9b97bd9b704f85f0184f7a213cc4d62bd9654c for pr-55982
Nov 17 11:05:39.004 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-55982/worker-5/master#6b9b97bd9b704f85f0184f7a213cc4d62bd9654c:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-55982/master#6b9b97bd9b704f85f0184f7a213cc4d62bd9654c:/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 +6b9b97bd9b704f85f0184f7a213cc4d62bd9654c-alt build --frozen" "-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 17 11:05:39.459 INFO [stdout] 52b365d9259aa8441336a2091bb5fc06a0abbe7a5bf374bfbcfa4cf51336b503
Nov 17 11:05:39.461 INFO running `"docker" "start" "-a" "52b365d9259aa8441336a2091bb5fc06a0abbe7a5bf374bfbcfa4cf51336b503"`
Nov 17 11:05:41.229 INFO [stderr] usermod: no changes
Nov 17 11:05:41.493 INFO [stderr]    Compiling ieee754 v0.2.2
Nov 17 11:05:41.494 INFO [stderr]    Compiling fs-utils v1.0.0
Nov 17 11:05:44.141 INFO [stderr]    Compiling rust-htslib v0.15.0
Nov 17 11:06:35.688 INFO [stderr]    Compiling consensus v0.1.0 (/source)
Nov 17 11:06:37.095 INFO [stderr] warning: unused import: `std::env`
Nov 17 11:06:37.096 INFO [stderr]   --> src/main.rs:12:5
Nov 17 11:06:37.097 INFO [stderr]    |
Nov 17 11:06:37.097 INFO [stderr] 12 | use std::env;
Nov 17 11:06:37.097 INFO [stderr]    |     ^^^^^^^^
Nov 17 11:06:37.098 INFO [stderr]    |
Nov 17 11:06:37.098 INFO [stderr]    = note: #[warn(unused_imports)] on by default
Nov 17 11:06:37.099 INFO [stderr] 
Nov 17 11:06:37.099 INFO [stderr] warning: unused import: `rust_htslib::prelude::*`
Nov 17 11:06:37.100 INFO [stderr]   --> src/main.rs:16:5
Nov 17 11:06:37.100 INFO [stderr]    |
Nov 17 11:06:37.100 INFO [stderr] 16 | use rust_htslib::prelude::*;
Nov 17 11:06:37.101 INFO [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.101 INFO [stderr] 
Nov 17 11:06:37.102 INFO [stderr] warning: unused import: `std::io`
Nov 17 11:06:37.102 INFO [stderr]   --> src/main.rs:21:5
Nov 17 11:06:37.102 INFO [stderr]    |
Nov 17 11:06:37.103 INFO [stderr] 21 | use std::io;
Nov 17 11:06:37.103 INFO [stderr]    |     ^^^^^^^
Nov 17 11:06:37.103 INFO [stderr] 
Nov 17 11:06:37.103 INFO [stderr] warning: unused import: `PathBuf`
Nov 17 11:06:37.104 INFO [stderr]   --> src/main.rs:25:23
Nov 17 11:06:37.104 INFO [stderr]    |
Nov 17 11:06:37.104 INFO [stderr] 25 | use std::path::{Path, PathBuf};
Nov 17 11:06:37.105 INFO [stderr]    |                       ^^^^^^^
Nov 17 11:06:37.105 INFO [stderr] 
Nov 17 11:06:37.105 INFO [stderr] warning: unused import: `SubCommand`
Nov 17 11:06:37.105 INFO [stderr]   --> src/main.rs:26:22
Nov 17 11:06:37.106 INFO [stderr]    |
Nov 17 11:06:37.106 INFO [stderr] 26 | use clap::{Arg, App, SubCommand};
Nov 17 11:06:37.106 INFO [stderr]    |                      ^^^^^^^^^^
Nov 17 11:06:37.109 INFO [stderr] 
Nov 17 11:06:37.109 INFO [stderr] warning: unnecessary parentheses around `if` condition
Nov 17 11:06:37.109 INFO [stderr]    --> src/main.rs:218:20
Nov 17 11:06:37.110 INFO [stderr]     |
Nov 17 11:06:37.110 INFO [stderr] 218 |                 if (num_position[&(i as usize)] == num_position[&(0 as usize)]) {
Nov 17 11:06:37.110 INFO [stderr]     |                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Nov 17 11:06:37.110 INFO [stderr]     |
Nov 17 11:06:37.111 INFO [stderr]     = note: #[warn(unused_parens)] on by default
Nov 17 11:06:37.111 INFO [stderr] 
Nov 17 11:06:37.111 INFO [stderr] warning: unnecessary parentheses around `if` condition
Nov 17 11:06:37.112 INFO [stderr]    --> src/main.rs:239:16
Nov 17 11:06:37.112 INFO [stderr]     |
Nov 17 11:06:37.112 INFO [stderr] 239 |             if (baseEach_percent_record.len() > 0) {
Nov 17 11:06:37.112 INFO [stderr]     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Nov 17 11:06:37.113 INFO [stderr] 
Nov 17 11:06:37.267 INFO [stderr] warning: unused import: `std::io::prelude`
Nov 17 11:06:37.267 INFO [stderr]   --> src/main.rs:22:5
Nov 17 11:06:37.267 INFO [stderr]    |
Nov 17 11:06:37.267 INFO [stderr] 22 | use std::io::prelude::*;
Nov 17 11:06:37.267 INFO [stderr]    |     ^^^^^^^^^^^^^^^^
Nov 17 11:06:37.267 INFO [stderr] 
Nov 17 11:06:37.279 INFO [stderr] warning: unused variable: `consensus_base`
Nov 17 11:06:37.279 INFO [stderr]    --> src/main.rs:139:9
Nov 17 11:06:37.279 INFO [stderr]     |
Nov 17 11:06:37.279 INFO [stderr] 139 |     let consensus_base:Vec<u8> = Vec::new();
Nov 17 11:06:37.279 INFO [stderr]     |         ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead
Nov 17 11:06:37.279 INFO [stderr]     |
Nov 17 11:06:37.279 INFO [stderr]     = note: #[warn(unused_variables)] on by default
Nov 17 11:06:37.279 INFO [stderr] 
Nov 17 11:06:37.287 INFO [stderr] warning: unused variable: `consensus_source_reads`
Nov 17 11:06:37.287 INFO [stderr]    --> src/main.rs:144:13
Nov 17 11:06:37.287 INFO [stderr]     |
Nov 17 11:06:37.287 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Nov 17 11:06:37.287 INFO [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead
Nov 17 11:06:37.287 INFO [stderr] 
Nov 17 11:06:37.287 INFO [stderr] warning: unused variable: `chrom`
Nov 17 11:06:37.287 INFO [stderr]    --> src/main.rs:283:121
Nov 17 11:06:37.287 INFO [stderr]     |
Nov 17 11:06:37.287 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) {
Nov 17 11:06:37.287 INFO [stderr]     |                                                                                                                         ^^^^^ help: consider using `_chrom` instead
Nov 17 11:06:37.287 INFO [stderr] 
Nov 17 11:06:37.287 INFO [stderr] warning: value assigned to `new_seq_b` is never read
Nov 17 11:06:37.287 INFO [stderr]    --> src/main.rs:370:21
Nov 17 11:06:37.287 INFO [stderr]     |
Nov 17 11:06:37.287 INFO [stderr] 370 |             let mut new_seq_b:Vec<u8> = Vec::new();
Nov 17 11:06:37.287 INFO [stderr]     |                     ^^^^^^^^^
Nov 17 11:06:37.287 INFO [stderr]     |
Nov 17 11:06:37.287 INFO [stderr]     = note: #[warn(unused_assignments)] on by default
Nov 17 11:06:37.287 INFO [stderr] 
Nov 17 11:06:37.303 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:37.303 INFO [stderr]   --> src/main.rs:74:9
Nov 17 11:06:37.303 INFO [stderr]    |
Nov 17 11:06:37.303 INFO [stderr] 74 |     let mut pair;
Nov 17 11:06:37.303 INFO [stderr]    |         ----^^^^
Nov 17 11:06:37.303 INFO [stderr]    |         |
Nov 17 11:06:37.303 INFO [stderr]    |         help: remove this `mut`
Nov 17 11:06:37.303 INFO [stderr]    |
Nov 17 11:06:37.303 INFO [stderr]    = note: #[warn(unused_mut)] on by default
Nov 17 11:06:37.303 INFO [stderr] 
Nov 17 11:06:37.303 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:37.303 INFO [stderr]   --> src/main.rs:75:9
Nov 17 11:06:37.303 INFO [stderr]    |
Nov 17 11:06:37.303 INFO [stderr] 75 |     let mut strand;
Nov 17 11:06:37.303 INFO [stderr]    |         ----^^^^^^
Nov 17 11:06:37.303 INFO [stderr]    |         |
Nov 17 11:06:37.303 INFO [stderr]    |         help: remove this `mut`
Nov 17 11:06:37.303 INFO [stderr] 
Nov 17 11:06:37.303 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:37.303 INFO [stderr]   --> src/main.rs:76:9
Nov 17 11:06:37.303 INFO [stderr]    |
Nov 17 11:06:37.303 INFO [stderr] 76 |     let mut aln_pos;
Nov 17 11:06:37.303 INFO [stderr]    |         ----^^^^^^^
Nov 17 11:06:37.303 INFO [stderr]    |         |
Nov 17 11:06:37.303 INFO [stderr]    |         help: remove this `mut`
Nov 17 11:06:37.303 INFO [stderr] 
Nov 17 11:06:37.343 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:37.343 INFO [stderr]    --> src/main.rs:144:9
Nov 17 11:06:37.343 INFO [stderr]     |
Nov 17 11:06:37.343 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Nov 17 11:06:37.343 INFO [stderr]     |         ----^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.343 INFO [stderr]     |         |
Nov 17 11:06:37.343 INFO [stderr]     |         help: remove this `mut`
Nov 17 11:06:37.343 INFO [stderr] 
Nov 17 11:06:37.343 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:37.343 INFO [stderr]    --> src/main.rs:151:9
Nov 17 11:06:37.343 INFO [stderr]     |
Nov 17 11:06:37.343 INFO [stderr] 151 |     let mut top_cigar:&CigarStringView;
Nov 17 11:06:37.343 INFO [stderr]     |         ----^^^^^^^^^
Nov 17 11:06:37.343 INFO [stderr]     |         |
Nov 17 11:06:37.343 INFO [stderr]     |         help: remove this `mut`
Nov 17 11:06:37.343 INFO [stderr] 
Nov 17 11:06:37.373 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:37.373 INFO [stderr]    --> src/main.rs:338:9
Nov 17 11:06:37.373 INFO [stderr]     |
Nov 17 11:06:37.373 INFO [stderr] 338 |     let mut need_trim:bool;
Nov 17 11:06:37.373 INFO [stderr]     |         ----^^^^^^^^^
Nov 17 11:06:37.373 INFO [stderr]     |         |
Nov 17 11:06:37.373 INFO [stderr]     |         help: remove this `mut`
Nov 17 11:06:37.375 INFO [stderr] 
Nov 17 11:06:37.375 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:37.375 INFO [stderr]    --> src/main.rs:355:9
Nov 17 11:06:37.375 INFO [stderr]     |
Nov 17 11:06:37.375 INFO [stderr] 355 |     let mut chrom = 0;
Nov 17 11:06:37.375 INFO [stderr]     |         ----^^^^^
Nov 17 11:06:37.375 INFO [stderr]     |         |
Nov 17 11:06:37.375 INFO [stderr]     |         help: remove this `mut`
Nov 17 11:06:37.375 INFO [stderr] 
Nov 17 11:06:37.390 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse`
Nov 17 11:06:37.390 INFO [stderr]   --> src/main.rs:68:1
Nov 17 11:06:37.390 INFO [stderr]    |
Nov 17 11:06:37.390 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){
Nov 17 11:06:37.390 INFO [stderr] 69 | |
Nov 17 11:06:37.390 INFO [stderr] 70 | |     let qname_str = String::from_utf8_lossy(record.qname()).to_string();
Nov 17 11:06:37.390 INFO [stderr] 71 | |     let temp_v:Vec<&str> = qname_str.split('#').collect();
Nov 17 11:06:37.390 INFO [stderr] ...  |
Nov 17 11:06:37.390 INFO [stderr] 97 | |     (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos)
Nov 17 11:06:37.390 INFO [stderr] 98 | | }
Nov 17 11:06:37.390 INFO [stderr]    | |_^
Nov 17 11:06:37.390 INFO [stderr]    |
Nov 17 11:06:37.390 INFO [stderr]    = note: #[warn(non_snake_case)] on by default
Nov 17 11:06:37.390 INFO [stderr] 
Nov 17 11:06:37.390 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record`
Nov 17 11:06:37.390 INFO [stderr]    --> src/main.rs:147:9
Nov 17 11:06:37.390 INFO [stderr]     |
Nov 17 11:06:37.390 INFO [stderr] 147 |     let mut baseEach_num_record = String::new();
Nov 17 11:06:37.390 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.390 INFO [stderr] 
Nov 17 11:06:37.399 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record`
Nov 17 11:06:37.399 INFO [stderr]    --> src/main.rs:148:9
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.399 INFO [stderr] 148 |     let mut baseEach_percent_record = String::new();
Nov 17 11:06:37.399 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.399 INFO [stderr] 
Nov 17 11:06:37.399 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:37.399 INFO [stderr]    --> src/main.rs:267:9
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.399 INFO [stderr] 267 |         o_buff.write(&member_record.2);
Nov 17 11:06:37.399 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.399 INFO [stderr]     = note: #[warn(unused_must_use)] on by default
Nov 17 11:06:37.399 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:37.399 INFO [stderr] 
Nov 17 11:06:37.399 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:37.399 INFO [stderr]    --> src/main.rs:269:9
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.399 INFO [stderr] 269 |         o_buff.write(&member_record.0);
Nov 17 11:06:37.399 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.399 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:37.399 INFO [stderr] 
Nov 17 11:06:37.399 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:37.399 INFO [stderr]    --> src/main.rs:272:9
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.399 INFO [stderr] 272 |         o_buff.write(&real_qual_temp);
Nov 17 11:06:37.399 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.399 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:37.399 INFO [stderr] 
Nov 17 11:06:37.399 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:37.399 INFO [stderr]    --> src/main.rs:274:5
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.399 INFO [stderr] 274 |     o_buff.write(b"\n");
Nov 17 11:06:37.399 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.399 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:37.399 INFO [stderr] 
Nov 17 11:06:37.399 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:37.399 INFO [stderr]    --> src/main.rs:277:5
Nov 17 11:06:37.399 INFO [stderr]     |
Nov 17 11:06:37.400 INFO [stderr] 277 |     o_buff.write(b"\n");
Nov 17 11:06:37.400 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.400 INFO [stderr]     |
Nov 17 11:06:37.400 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:37.400 INFO [stderr] 
Nov 17 11:06:37.400 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:37.400 INFO [stderr]    --> src/main.rs:280:5
Nov 17 11:06:37.400 INFO [stderr]     |
Nov 17 11:06:37.400 INFO [stderr] 280 |     o_buff.write(b"\n");
Nov 17 11:06:37.400 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.400 INFO [stderr]     |
Nov 17 11:06:37.400 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:37.400 INFO [stderr] 
Nov 17 11:06:37.400 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Nov 17 11:06:37.400 INFO [stderr]    --> src/main.rs:286:10
Nov 17 11:06:37.400 INFO [stderr]     |
Nov 17 11:06:37.400 INFO [stderr] 286 |     for (key_dupGroup, pair_dup) in pd.iter() {
Nov 17 11:06:37.400 INFO [stderr]     |          ^^^^^^^^^^^^
Nov 17 11:06:37.400 INFO [stderr] 
Nov 17 11:06:37.400 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group`
Nov 17 11:06:37.400 INFO [stderr]    --> src/main.rs:357:9
Nov 17 11:06:37.400 INFO [stderr]     |
Nov 17 11:06:37.400 INFO [stderr] 357 |     let mut position_dupGroup: HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>> = HashMap::new();
Nov 17 11:06:37.400 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:37.400 INFO [stderr] 
Nov 17 11:06:37.400 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Nov 17 11:06:37.400 INFO [stderr]    --> src/main.rs:387:17
Nov 17 11:06:37.400 INFO [stderr]     |
Nov 17 11:06:37.400 INFO [stderr] 387 |             let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size);
Nov 17 11:06:37.400 INFO [stderr]     |                 ^^^^^^^^^^^^
Nov 17 11:06:37.400 INFO [stderr] 
Nov 17 11:06:41.406 INFO [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 1m 00s
Nov 17 11:06:41.406 INFO [stderr] su: No module specific data is present
Nov 17 11:06:42.023 INFO running `"docker" "inspect" "52b365d9259aa8441336a2091bb5fc06a0abbe7a5bf374bfbcfa4cf51336b503"`
Nov 17 11:06:42.603 INFO running `"docker" "rm" "-f" "52b365d9259aa8441336a2091bb5fc06a0abbe7a5bf374bfbcfa4cf51336b503"`
Nov 17 11:06:43.019 INFO [stdout] 52b365d9259aa8441336a2091bb5fc06a0abbe7a5bf374bfbcfa4cf51336b503
Nov 17 11:06:43.027 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-55982/worker-5/master#6b9b97bd9b704f85f0184f7a213cc4d62bd9654c:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-55982/master#6b9b97bd9b704f85f0184f7a213cc4d62bd9654c:/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 +6b9b97bd9b704f85f0184f7a213cc4d62bd9654c-alt test --frozen --no-run" "-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 17 11:06:43.607 INFO [stdout] 994faf3afda80c9d7d5f1ed569f96814aaad9cf4ec0811cf7fc7ac39401f4577
Nov 17 11:06:43.610 INFO running `"docker" "start" "-a" "994faf3afda80c9d7d5f1ed569f96814aaad9cf4ec0811cf7fc7ac39401f4577"`
Nov 17 11:06:45.291 INFO [stderr] usermod: no changes
Nov 17 11:06:45.542 INFO [stderr]    Compiling consensus v0.1.0 (/source)
Nov 17 11:06:47.607 INFO [stderr] warning: unused import: `std::env`
Nov 17 11:06:47.607 INFO [stderr]   --> src/main.rs:12:5
Nov 17 11:06:47.607 INFO [stderr]    |
Nov 17 11:06:47.607 INFO [stderr] 12 | use std::env;
Nov 17 11:06:47.607 INFO [stderr]    |     ^^^^^^^^
Nov 17 11:06:47.607 INFO [stderr]    |
Nov 17 11:06:47.607 INFO [stderr]    = note: #[warn(unused_imports)] on by default
Nov 17 11:06:47.607 INFO [stderr] 
Nov 17 11:06:47.607 INFO [stderr] warning: unused import: `rust_htslib::prelude::*`
Nov 17 11:06:47.607 INFO [stderr]   --> src/main.rs:16:5
Nov 17 11:06:47.607 INFO [stderr]    |
Nov 17 11:06:47.607 INFO [stderr] 16 | use rust_htslib::prelude::*;
Nov 17 11:06:47.607 INFO [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.607 INFO [stderr] 
Nov 17 11:06:47.607 INFO [stderr] warning: unused import: `std::io`
Nov 17 11:06:47.607 INFO [stderr]   --> src/main.rs:21:5
Nov 17 11:06:47.607 INFO [stderr]    |
Nov 17 11:06:47.607 INFO [stderr] 21 | use std::io;
Nov 17 11:06:47.607 INFO [stderr]    |     ^^^^^^^
Nov 17 11:06:47.607 INFO [stderr] 
Nov 17 11:06:47.607 INFO [stderr] warning: unused import: `PathBuf`
Nov 17 11:06:47.607 INFO [stderr]   --> src/main.rs:25:23
Nov 17 11:06:47.607 INFO [stderr]    |
Nov 17 11:06:47.607 INFO [stderr] 25 | use std::path::{Path, PathBuf};
Nov 17 11:06:47.607 INFO [stderr]    |                       ^^^^^^^
Nov 17 11:06:47.607 INFO [stderr] 
Nov 17 11:06:47.607 INFO [stderr] warning: unused import: `SubCommand`
Nov 17 11:06:47.607 INFO [stderr]   --> src/main.rs:26:22
Nov 17 11:06:47.607 INFO [stderr]    |
Nov 17 11:06:47.607 INFO [stderr] 26 | use clap::{Arg, App, SubCommand};
Nov 17 11:06:47.607 INFO [stderr]    |                      ^^^^^^^^^^
Nov 17 11:06:47.607 INFO [stderr] 
Nov 17 11:06:47.607 INFO [stderr] warning: unnecessary parentheses around `if` condition
Nov 17 11:06:47.607 INFO [stderr]    --> src/main.rs:218:20
Nov 17 11:06:47.607 INFO [stderr]     |
Nov 17 11:06:47.607 INFO [stderr] 218 |                 if (num_position[&(i as usize)] == num_position[&(0 as usize)]) {
Nov 17 11:06:47.607 INFO [stderr]     |                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Nov 17 11:06:47.607 INFO [stderr]     |
Nov 17 11:06:47.607 INFO [stderr]     = note: #[warn(unused_parens)] on by default
Nov 17 11:06:47.607 INFO [stderr] 
Nov 17 11:06:47.607 INFO [stderr] warning: unnecessary parentheses around `if` condition
Nov 17 11:06:47.607 INFO [stderr]    --> src/main.rs:239:16
Nov 17 11:06:47.607 INFO [stderr]     |
Nov 17 11:06:47.607 INFO [stderr] 239 |             if (baseEach_percent_record.len() > 0) {
Nov 17 11:06:47.607 INFO [stderr]     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Nov 17 11:06:47.608 INFO [stderr] 
Nov 17 11:06:47.795 INFO [stderr] warning: unused import: `std::io::prelude`
Nov 17 11:06:47.795 INFO [stderr]   --> src/main.rs:22:5
Nov 17 11:06:47.795 INFO [stderr]    |
Nov 17 11:06:47.795 INFO [stderr] 22 | use std::io::prelude::*;
Nov 17 11:06:47.795 INFO [stderr]    |     ^^^^^^^^^^^^^^^^
Nov 17 11:06:47.795 INFO [stderr] 
Nov 17 11:06:47.812 INFO [stderr] warning: unused variable: `consensus_base`
Nov 17 11:06:47.812 INFO [stderr]    --> src/main.rs:139:9
Nov 17 11:06:47.812 INFO [stderr]     |
Nov 17 11:06:47.812 INFO [stderr] 139 |     let consensus_base:Vec<u8> = Vec::new();
Nov 17 11:06:47.812 INFO [stderr]     |         ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead
Nov 17 11:06:47.812 INFO [stderr]     |
Nov 17 11:06:47.812 INFO [stderr]     = note: #[warn(unused_variables)] on by default
Nov 17 11:06:47.812 INFO [stderr] 
Nov 17 11:06:47.812 INFO [stderr] warning: unused variable: `consensus_source_reads`
Nov 17 11:06:47.812 INFO [stderr]    --> src/main.rs:144:13
Nov 17 11:06:47.812 INFO [stderr]     |
Nov 17 11:06:47.812 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Nov 17 11:06:47.812 INFO [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead
Nov 17 11:06:47.812 INFO [stderr] 
Nov 17 11:06:47.812 INFO [stderr] warning: unused variable: `chrom`
Nov 17 11:06:47.812 INFO [stderr]    --> src/main.rs:283:121
Nov 17 11:06:47.812 INFO [stderr]     |
Nov 17 11:06:47.812 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) {
Nov 17 11:06:47.812 INFO [stderr]     |                                                                                                                         ^^^^^ help: consider using `_chrom` instead
Nov 17 11:06:47.812 INFO [stderr] 
Nov 17 11:06:47.812 INFO [stderr] warning: value assigned to `new_seq_b` is never read
Nov 17 11:06:47.812 INFO [stderr]    --> src/main.rs:370:21
Nov 17 11:06:47.812 INFO [stderr]     |
Nov 17 11:06:47.812 INFO [stderr] 370 |             let mut new_seq_b:Vec<u8> = Vec::new();
Nov 17 11:06:47.812 INFO [stderr]     |                     ^^^^^^^^^
Nov 17 11:06:47.819 INFO [stderr]     |
Nov 17 11:06:47.819 INFO [stderr]     = note: #[warn(unused_assignments)] on by default
Nov 17 11:06:47.819 INFO [stderr] 
Nov 17 11:06:47.833 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:47.833 INFO [stderr]   --> src/main.rs:74:9
Nov 17 11:06:47.833 INFO [stderr]    |
Nov 17 11:06:47.833 INFO [stderr] 74 |     let mut pair;
Nov 17 11:06:47.833 INFO [stderr]    |         ----^^^^
Nov 17 11:06:47.833 INFO [stderr]    |         |
Nov 17 11:06:47.833 INFO [stderr]    |         help: remove this `mut`
Nov 17 11:06:47.833 INFO [stderr]    |
Nov 17 11:06:47.833 INFO [stderr]    = note: #[warn(unused_mut)] on by default
Nov 17 11:06:47.833 INFO [stderr] 
Nov 17 11:06:47.833 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:47.833 INFO [stderr]   --> src/main.rs:75:9
Nov 17 11:06:47.833 INFO [stderr]    |
Nov 17 11:06:47.833 INFO [stderr] 75 |     let mut strand;
Nov 17 11:06:47.833 INFO [stderr]    |         ----^^^^^^
Nov 17 11:06:47.833 INFO [stderr]    |         |
Nov 17 11:06:47.833 INFO [stderr]    |         help: remove this `mut`
Nov 17 11:06:47.833 INFO [stderr] 
Nov 17 11:06:47.833 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:47.833 INFO [stderr]   --> src/main.rs:76:9
Nov 17 11:06:47.833 INFO [stderr]    |
Nov 17 11:06:47.833 INFO [stderr] 76 |     let mut aln_pos;
Nov 17 11:06:47.833 INFO [stderr]    |         ----^^^^^^^
Nov 17 11:06:47.833 INFO [stderr]    |         |
Nov 17 11:06:47.833 INFO [stderr]    |         help: remove this `mut`
Nov 17 11:06:47.833 INFO [stderr] 
Nov 17 11:06:47.868 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:47.868 INFO [stderr]    --> src/main.rs:144:9
Nov 17 11:06:47.868 INFO [stderr]     |
Nov 17 11:06:47.869 INFO [stderr] 144 |     let mut consensus_source_reads = String::new();
Nov 17 11:06:47.869 INFO [stderr]     |         ----^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.869 INFO [stderr]     |         |
Nov 17 11:06:47.869 INFO [stderr]     |         help: remove this `mut`
Nov 17 11:06:47.870 INFO [stderr] 
Nov 17 11:06:47.870 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:47.870 INFO [stderr]    --> src/main.rs:151:9
Nov 17 11:06:47.870 INFO [stderr]     |
Nov 17 11:06:47.870 INFO [stderr] 151 |     let mut top_cigar:&CigarStringView;
Nov 17 11:06:47.870 INFO [stderr]     |         ----^^^^^^^^^
Nov 17 11:06:47.870 INFO [stderr]     |         |
Nov 17 11:06:47.870 INFO [stderr]     |         help: remove this `mut`
Nov 17 11:06:47.870 INFO [stderr] 
Nov 17 11:06:47.886 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:47.886 INFO [stderr]    --> src/main.rs:338:9
Nov 17 11:06:47.886 INFO [stderr]     |
Nov 17 11:06:47.886 INFO [stderr] 338 |     let mut need_trim:bool;
Nov 17 11:06:47.886 INFO [stderr]     |         ----^^^^^^^^^
Nov 17 11:06:47.886 INFO [stderr]     |         |
Nov 17 11:06:47.886 INFO [stderr]     |         help: remove this `mut`
Nov 17 11:06:47.886 INFO [stderr] 
Nov 17 11:06:47.886 INFO [stderr] warning: variable does not need to be mutable
Nov 17 11:06:47.886 INFO [stderr]    --> src/main.rs:355:9
Nov 17 11:06:47.886 INFO [stderr]     |
Nov 17 11:06:47.886 INFO [stderr] 355 |     let mut chrom = 0;
Nov 17 11:06:47.886 INFO [stderr]     |         ----^^^^^
Nov 17 11:06:47.886 INFO [stderr]     |         |
Nov 17 11:06:47.886 INFO [stderr]     |         help: remove this `mut`
Nov 17 11:06:47.886 INFO [stderr] 
Nov 17 11:06:47.899 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse`
Nov 17 11:06:47.899 INFO [stderr]   --> src/main.rs:68:1
Nov 17 11:06:47.899 INFO [stderr]    |
Nov 17 11:06:47.899 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){
Nov 17 11:06:47.899 INFO [stderr] 69 | |
Nov 17 11:06:47.899 INFO [stderr] 70 | |     let qname_str = String::from_utf8_lossy(record.qname()).to_string();
Nov 17 11:06:47.899 INFO [stderr] 71 | |     let temp_v:Vec<&str> = qname_str.split('#').collect();
Nov 17 11:06:47.899 INFO [stderr] ...  |
Nov 17 11:06:47.899 INFO [stderr] 97 | |     (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos)
Nov 17 11:06:47.899 INFO [stderr] 98 | | }
Nov 17 11:06:47.899 INFO [stderr]    | |_^
Nov 17 11:06:47.899 INFO [stderr]    |
Nov 17 11:06:47.899 INFO [stderr]    = note: #[warn(non_snake_case)] on by default
Nov 17 11:06:47.899 INFO [stderr] 
Nov 17 11:06:47.899 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record`
Nov 17 11:06:47.899 INFO [stderr]    --> src/main.rs:147:9
Nov 17 11:06:47.899 INFO [stderr]     |
Nov 17 11:06:47.899 INFO [stderr] 147 |     let mut baseEach_num_record = String::new();
Nov 17 11:06:47.899 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.899 INFO [stderr] 
Nov 17 11:06:47.899 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record`
Nov 17 11:06:47.899 INFO [stderr]    --> src/main.rs:148:9
Nov 17 11:06:47.899 INFO [stderr]     |
Nov 17 11:06:47.899 INFO [stderr] 148 |     let mut baseEach_percent_record = String::new();
Nov 17 11:06:47.899 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.899 INFO [stderr] 
Nov 17 11:06:47.900 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:47.900 INFO [stderr]    --> src/main.rs:267:9
Nov 17 11:06:47.900 INFO [stderr]     |
Nov 17 11:06:47.900 INFO [stderr] 267 |         o_buff.write(&member_record.2);
Nov 17 11:06:47.900 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.900 INFO [stderr]     |
Nov 17 11:06:47.900 INFO [stderr]     = note: #[warn(unused_must_use)] on by default
Nov 17 11:06:47.900 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:47.900 INFO [stderr] 
Nov 17 11:06:47.900 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:47.900 INFO [stderr]    --> src/main.rs:269:9
Nov 17 11:06:47.900 INFO [stderr]     |
Nov 17 11:06:47.900 INFO [stderr] 269 |         o_buff.write(&member_record.0);
Nov 17 11:06:47.901 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.901 INFO [stderr]     |
Nov 17 11:06:47.901 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:47.901 INFO [stderr] 
Nov 17 11:06:47.901 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:47.901 INFO [stderr]    --> src/main.rs:272:9
Nov 17 11:06:47.901 INFO [stderr]     |
Nov 17 11:06:47.901 INFO [stderr] 272 |         o_buff.write(&real_qual_temp);
Nov 17 11:06:47.901 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.901 INFO [stderr]     |
Nov 17 11:06:47.901 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:47.902 INFO [stderr] 
Nov 17 11:06:47.902 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:47.902 INFO [stderr]    --> src/main.rs:274:5
Nov 17 11:06:47.902 INFO [stderr]     |
Nov 17 11:06:47.902 INFO [stderr] 274 |     o_buff.write(b"\n");
Nov 17 11:06:47.902 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.902 INFO [stderr]     |
Nov 17 11:06:47.902 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:47.902 INFO [stderr] 
Nov 17 11:06:47.902 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:47.902 INFO [stderr]    --> src/main.rs:277:5
Nov 17 11:06:47.902 INFO [stderr]     |
Nov 17 11:06:47.902 INFO [stderr] 277 |     o_buff.write(b"\n");
Nov 17 11:06:47.902 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.903 INFO [stderr]     |
Nov 17 11:06:47.903 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:47.903 INFO [stderr] 
Nov 17 11:06:47.903 INFO [stderr] warning: unused `std::result::Result` that must be used
Nov 17 11:06:47.903 INFO [stderr]    --> src/main.rs:280:5
Nov 17 11:06:47.903 INFO [stderr]     |
Nov 17 11:06:47.903 INFO [stderr] 280 |     o_buff.write(b"\n");
Nov 17 11:06:47.903 INFO [stderr]     |     ^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.903 INFO [stderr]     |
Nov 17 11:06:47.903 INFO [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
Nov 17 11:06:47.903 INFO [stderr] 
Nov 17 11:06:47.903 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Nov 17 11:06:47.903 INFO [stderr]    --> src/main.rs:286:10
Nov 17 11:06:47.903 INFO [stderr]     |
Nov 17 11:06:47.903 INFO [stderr] 286 |     for (key_dupGroup, pair_dup) in pd.iter() {
Nov 17 11:06:47.903 INFO [stderr]     |          ^^^^^^^^^^^^
Nov 17 11:06:47.903 INFO [stderr] 
Nov 17 11:06:47.903 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group`
Nov 17 11:06:47.903 INFO [stderr]    --> src/main.rs:357:9
Nov 17 11:06:47.903 INFO [stderr]     |
Nov 17 11:06:47.903 INFO [stderr] 357 |     let mut position_dupGroup: HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>> = HashMap::new();
Nov 17 11:06:47.903 INFO [stderr]     |         ^^^^^^^^^^^^^^^^^^^^^
Nov 17 11:06:47.903 INFO [stderr] 
Nov 17 11:06:47.903 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Nov 17 11:06:47.903 INFO [stderr]    --> src/main.rs:387:17
Nov 17 11:06:47.903 INFO [stderr]     |
Nov 17 11:06:47.903 INFO [stderr] 387 |             let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size);
Nov 17 11:06:47.903 INFO [stderr]     |                 ^^^^^^^^^^^^
Nov 17 11:06:47.903 INFO [stderr] 
Nov 17 11:06:48.314 INFO [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 2.96s
Nov 17 11:06:48.321 INFO [stderr] su: No module specific data is present
Nov 17 11:06:49.287 INFO running `"docker" "inspect" "994faf3afda80c9d7d5f1ed569f96814aaad9cf4ec0811cf7fc7ac39401f4577"`
Nov 17 11:06:49.603 INFO running `"docker" "rm" "-f" "994faf3afda80c9d7d5f1ed569f96814aaad9cf4ec0811cf7fc7ac39401f4577"`
Nov 17 11:06:49.907 INFO [stdout] 994faf3afda80c9d7d5f1ed569f96814aaad9cf4ec0811cf7fc7ac39401f4577
Nov 17 11:06:49.915 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-55982/worker-5/master#6b9b97bd9b704f85f0184f7a213cc4d62bd9654c:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-55982/master#6b9b97bd9b704f85f0184f7a213cc4d62bd9654c:/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 +6b9b97bd9b704f85f0184f7a213cc4d62bd9654c-alt test --frozen" "-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 17 11:06:50.363 INFO [stdout] 386b80ac839a55b250d28b02ab32cba691845e20cdd543fd62d7f28673b1bf05
Nov 17 11:06:50.369 INFO running `"docker" "start" "-a" "386b80ac839a55b250d28b02ab32cba691845e20cdd543fd62d7f28673b1bf05"`
Nov 17 11:06:51.410 INFO [stderr] usermod: no changes
Nov 17 11:06:51.539 INFO [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 0.09s
Nov 17 11:06:51.551 INFO [stderr]      Running /target/debug/deps/consensus-41249b90fdfaa303
Nov 17 11:06:51.551 INFO [stdout] 
Nov 17 11:06:51.551 INFO [stdout] running 0 tests
Nov 17 11:06:51.551 INFO [stdout] 
Nov 17 11:06:51.551 INFO [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out
Nov 17 11:06:51.551 INFO [stdout] 
Nov 17 11:06:51.559 INFO [stderr] su: No module specific data is present
Nov 17 11:06:52.227 INFO running `"docker" "inspect" "386b80ac839a55b250d28b02ab32cba691845e20cdd543fd62d7f28673b1bf05"`
Nov 17 11:06:52.527 INFO running `"docker" "rm" "-f" "386b80ac839a55b250d28b02ab32cba691845e20cdd543fd62d7f28673b1bf05"`
Nov 17 11:06:52.975 INFO [stdout] 386b80ac839a55b250d28b02ab32cba691845e20cdd543fd62d7f28673b1bf05