Nov 01 17:16:27.348 INFO testing TuBieJun/consensus against beta-2018-10-30 for beta-1.31-1
Nov 01 17:16:27.348 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.31-1/worker-7/beta-2018-10-30:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-7/beta-1.31-1/beta-2018-10-30:/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 +beta-2018-10-30 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"`
Nov 01 17:16:27.972 INFO blam! 712394add6a976a87c5a507de288615e3edce4efda255c5f03561ba6f654b276
Nov 01 17:16:27.976 INFO running `"docker" "start" "-a" "712394add6a976a87c5a507de288615e3edce4efda255c5f03561ba6f654b276"`
Nov 01 17:16:29.467 INFO kablam! usermod: no changes
Nov 01 17:16:29.655 INFO kablam!    Compiling ieee754 v0.2.2
Nov 01 17:16:29.659 INFO kablam!    Compiling fs-utils v1.0.0
Nov 01 17:16:29.663 INFO kablam!    Compiling itertools v0.6.5
Nov 01 17:16:31.735 INFO kablam!    Compiling rust-htslib v0.15.0
Nov 01 17:17:03.844 INFO kablam!    Compiling consensus v0.1.0 (/source)
Nov 01 17:17:05.192 INFO kablam! warning: unused import: `std::env`
Nov 01 17:17:05.192 INFO kablam!   --> src/main.rs:12:5
Nov 01 17:17:05.192 INFO kablam!    |
Nov 01 17:17:05.193 INFO kablam! 12 | use std::env;
Nov 01 17:17:05.193 INFO kablam!    |     ^^^^^^^^
Nov 01 17:17:05.193 INFO kablam!    |
Nov 01 17:17:05.194 INFO kablam!    = note: #[warn(unused_imports)] on by default
Nov 01 17:17:05.194 INFO kablam! 
Nov 01 17:17:05.194 INFO kablam! warning: unused import: `rust_htslib::prelude::*`
Nov 01 17:17:05.194 INFO kablam!   --> src/main.rs:16:5
Nov 01 17:17:05.195 INFO kablam!    |
Nov 01 17:17:05.195 INFO kablam! 16 | use rust_htslib::prelude::*;
Nov 01 17:17:05.195 INFO kablam!    |     ^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.195 INFO kablam! 
Nov 01 17:17:05.195 INFO kablam! warning: unused import: `std::io`
Nov 01 17:17:05.196 INFO kablam!   --> src/main.rs:21:5
Nov 01 17:17:05.196 INFO kablam!    |
Nov 01 17:17:05.196 INFO kablam! 21 | use std::io;
Nov 01 17:17:05.196 INFO kablam!    |     ^^^^^^^
Nov 01 17:17:05.196 INFO kablam! 
Nov 01 17:17:05.196 INFO kablam! warning: unused import: `PathBuf`
Nov 01 17:17:05.196 INFO kablam!   --> src/main.rs:25:23
Nov 01 17:17:05.196 INFO kablam!    |
Nov 01 17:17:05.196 INFO kablam! 25 | use std::path::{Path, PathBuf};
Nov 01 17:17:05.196 INFO kablam!    |                       ^^^^^^^
Nov 01 17:17:05.196 INFO kablam! 
Nov 01 17:17:05.196 INFO kablam! warning: unused import: `SubCommand`
Nov 01 17:17:05.196 INFO kablam!   --> src/main.rs:26:22
Nov 01 17:17:05.196 INFO kablam!    |
Nov 01 17:17:05.196 INFO kablam! 26 | use clap::{Arg, App, SubCommand};
Nov 01 17:17:05.196 INFO kablam!    |                      ^^^^^^^^^^
Nov 01 17:17:05.196 INFO kablam! 
Nov 01 17:17:05.196 INFO kablam! warning: unnecessary parentheses around `if` condition
Nov 01 17:17:05.196 INFO kablam!    --> src/main.rs:218:20
Nov 01 17:17:05.196 INFO kablam!     |
Nov 01 17:17:05.196 INFO kablam! 218 |                 if (num_position[&(i as usize)] == num_position[&(0 as usize)]) {
Nov 01 17:17:05.196 INFO kablam!     |                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Nov 01 17:17:05.196 INFO kablam!     |
Nov 01 17:17:05.196 INFO kablam!     = note: #[warn(unused_parens)] on by default
Nov 01 17:17:05.196 INFO kablam! 
Nov 01 17:17:05.196 INFO kablam! warning: unnecessary parentheses around `if` condition
Nov 01 17:17:05.196 INFO kablam!    --> src/main.rs:239:16
Nov 01 17:17:05.196 INFO kablam!     |
Nov 01 17:17:05.196 INFO kablam! 239 |             if (baseEach_percent_record.len() > 0) {
Nov 01 17:17:05.196 INFO kablam!     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Nov 01 17:17:05.196 INFO kablam! 
Nov 01 17:17:05.332 INFO kablam! warning: unused import: `std::io::prelude`
Nov 01 17:17:05.332 INFO kablam!   --> src/main.rs:22:5
Nov 01 17:17:05.332 INFO kablam!    |
Nov 01 17:17:05.332 INFO kablam! 22 | use std::io::prelude::*;
Nov 01 17:17:05.332 INFO kablam!    |     ^^^^^^^^^^^^^^^^
Nov 01 17:17:05.332 INFO kablam! 
Nov 01 17:17:05.347 INFO kablam! warning: unused variable: `consensus_base`
Nov 01 17:17:05.347 INFO kablam!    --> src/main.rs:139:9
Nov 01 17:17:05.347 INFO kablam!     |
Nov 01 17:17:05.347 INFO kablam! 139 |     let consensus_base:Vec<u8> = Vec::new();
Nov 01 17:17:05.347 INFO kablam!     |         ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead
Nov 01 17:17:05.347 INFO kablam!     |
Nov 01 17:17:05.347 INFO kablam!     = note: #[warn(unused_variables)] on by default
Nov 01 17:17:05.347 INFO kablam! 
Nov 01 17:17:05.347 INFO kablam! warning: unused variable: `consensus_source_reads`
Nov 01 17:17:05.347 INFO kablam!    --> src/main.rs:144:13
Nov 01 17:17:05.347 INFO kablam!     |
Nov 01 17:17:05.347 INFO kablam! 144 |     let mut consensus_source_reads = String::new();
Nov 01 17:17:05.348 INFO kablam!     |             ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead
Nov 01 17:17:05.348 INFO kablam! 
Nov 01 17:17:05.348 INFO kablam! warning: unused variable: `chrom`
Nov 01 17:17:05.348 INFO kablam!    --> src/main.rs:283:121
Nov 01 17:17:05.348 INFO kablam!     |
Nov 01 17:17:05.348 INFO kablam! 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 01 17:17:05.348 INFO kablam!     |                                                                                                                         ^^^^^ help: consider using `_chrom` instead
Nov 01 17:17:05.348 INFO kablam! 
Nov 01 17:17:05.348 INFO kablam! warning: value assigned to `new_seq_b` is never read
Nov 01 17:17:05.348 INFO kablam!    --> src/main.rs:370:21
Nov 01 17:17:05.348 INFO kablam!     |
Nov 01 17:17:05.348 INFO kablam! 370 |             let mut new_seq_b:Vec<u8> = Vec::new();
Nov 01 17:17:05.348 INFO kablam!     |                     ^^^^^^^^^
Nov 01 17:17:05.348 INFO kablam!     |
Nov 01 17:17:05.348 INFO kablam!     = note: #[warn(unused_assignments)] on by default
Nov 01 17:17:05.348 INFO kablam! 
Nov 01 17:17:05.357 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:05.357 INFO kablam!   --> src/main.rs:74:9
Nov 01 17:17:05.357 INFO kablam!    |
Nov 01 17:17:05.357 INFO kablam! 74 |     let mut pair;
Nov 01 17:17:05.357 INFO kablam!    |         ----^^^^
Nov 01 17:17:05.357 INFO kablam!    |         |
Nov 01 17:17:05.357 INFO kablam!    |         help: remove this `mut`
Nov 01 17:17:05.357 INFO kablam!    |
Nov 01 17:17:05.357 INFO kablam!    = note: #[warn(unused_mut)] on by default
Nov 01 17:17:05.357 INFO kablam! 
Nov 01 17:17:05.357 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:05.357 INFO kablam!   --> src/main.rs:75:9
Nov 01 17:17:05.357 INFO kablam!    |
Nov 01 17:17:05.357 INFO kablam! 75 |     let mut strand;
Nov 01 17:17:05.357 INFO kablam!    |         ----^^^^^^
Nov 01 17:17:05.357 INFO kablam!    |         |
Nov 01 17:17:05.357 INFO kablam!    |         help: remove this `mut`
Nov 01 17:17:05.357 INFO kablam! 
Nov 01 17:17:05.357 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:05.357 INFO kablam!   --> src/main.rs:76:9
Nov 01 17:17:05.357 INFO kablam!    |
Nov 01 17:17:05.357 INFO kablam! 76 |     let mut aln_pos;
Nov 01 17:17:05.357 INFO kablam!    |         ----^^^^^^^
Nov 01 17:17:05.357 INFO kablam!    |         |
Nov 01 17:17:05.357 INFO kablam!    |         help: remove this `mut`
Nov 01 17:17:05.357 INFO kablam! 
Nov 01 17:17:05.391 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:05.391 INFO kablam!    --> src/main.rs:144:9
Nov 01 17:17:05.392 INFO kablam!     |
Nov 01 17:17:05.392 INFO kablam! 144 |     let mut consensus_source_reads = String::new();
Nov 01 17:17:05.392 INFO kablam!     |         ----^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.392 INFO kablam!     |         |
Nov 01 17:17:05.392 INFO kablam!     |         help: remove this `mut`
Nov 01 17:17:05.392 INFO kablam! 
Nov 01 17:17:05.392 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:05.392 INFO kablam!    --> src/main.rs:151:9
Nov 01 17:17:05.392 INFO kablam!     |
Nov 01 17:17:05.392 INFO kablam! 151 |     let mut top_cigar:&CigarStringView;
Nov 01 17:17:05.392 INFO kablam!     |         ----^^^^^^^^^
Nov 01 17:17:05.392 INFO kablam!     |         |
Nov 01 17:17:05.392 INFO kablam!     |         help: remove this `mut`
Nov 01 17:17:05.392 INFO kablam! 
Nov 01 17:17:05.405 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:05.405 INFO kablam!    --> src/main.rs:338:9
Nov 01 17:17:05.405 INFO kablam!     |
Nov 01 17:17:05.405 INFO kablam! 338 |     let mut need_trim:bool;
Nov 01 17:17:05.405 INFO kablam!     |         ----^^^^^^^^^
Nov 01 17:17:05.405 INFO kablam!     |         |
Nov 01 17:17:05.405 INFO kablam!     |         help: remove this `mut`
Nov 01 17:17:05.411 INFO kablam! 
Nov 01 17:17:05.411 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:05.411 INFO kablam!    --> src/main.rs:355:9
Nov 01 17:17:05.411 INFO kablam!     |
Nov 01 17:17:05.411 INFO kablam! 355 |     let mut chrom = 0;
Nov 01 17:17:05.411 INFO kablam!     |         ----^^^^^
Nov 01 17:17:05.411 INFO kablam!     |         |
Nov 01 17:17:05.411 INFO kablam!     |         help: remove this `mut`
Nov 01 17:17:05.411 INFO kablam! 
Nov 01 17:17:05.423 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse`
Nov 01 17:17:05.423 INFO kablam!   --> src/main.rs:68:1
Nov 01 17:17:05.423 INFO kablam!    |
Nov 01 17:17:05.423 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){
Nov 01 17:17:05.423 INFO kablam! 69 | |
Nov 01 17:17:05.423 INFO kablam! 70 | |     let qname_str = String::from_utf8_lossy(record.qname()).to_string();
Nov 01 17:17:05.423 INFO kablam! 71 | |     let temp_v:Vec<&str> = qname_str.split('#').collect();
Nov 01 17:17:05.423 INFO kablam! ...  |
Nov 01 17:17:05.423 INFO kablam! 97 | |     (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos)
Nov 01 17:17:05.423 INFO kablam! 98 | | }
Nov 01 17:17:05.423 INFO kablam!    | |_^
Nov 01 17:17:05.424 INFO kablam!    |
Nov 01 17:17:05.424 INFO kablam!    = note: #[warn(non_snake_case)] on by default
Nov 01 17:17:05.424 INFO kablam! 
Nov 01 17:17:05.424 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record`
Nov 01 17:17:05.424 INFO kablam!    --> src/main.rs:147:9
Nov 01 17:17:05.424 INFO kablam!     |
Nov 01 17:17:05.424 INFO kablam! 147 |     let mut baseEach_num_record = String::new();
Nov 01 17:17:05.424 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.424 INFO kablam! 
Nov 01 17:17:05.424 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record`
Nov 01 17:17:05.424 INFO kablam!    --> src/main.rs:148:9
Nov 01 17:17:05.424 INFO kablam!     |
Nov 01 17:17:05.424 INFO kablam! 148 |     let mut baseEach_percent_record = String::new();
Nov 01 17:17:05.424 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.424 INFO kablam! 
Nov 01 17:17:05.424 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:05.425 INFO kablam!    --> src/main.rs:267:9
Nov 01 17:17:05.425 INFO kablam!     |
Nov 01 17:17:05.425 INFO kablam! 267 |         o_buff.write(&member_record.2);
Nov 01 17:17:05.425 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.425 INFO kablam!     |
Nov 01 17:17:05.425 INFO kablam!     = note: #[warn(unused_must_use)] on by default
Nov 01 17:17:05.425 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:05.425 INFO kablam! 
Nov 01 17:17:05.425 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:05.425 INFO kablam!    --> src/main.rs:269:9
Nov 01 17:17:05.425 INFO kablam!     |
Nov 01 17:17:05.425 INFO kablam! 269 |         o_buff.write(&member_record.0);
Nov 01 17:17:05.425 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.425 INFO kablam!     |
Nov 01 17:17:05.425 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:05.425 INFO kablam! 
Nov 01 17:17:05.425 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:05.425 INFO kablam!    --> src/main.rs:272:9
Nov 01 17:17:05.425 INFO kablam!     |
Nov 01 17:17:05.425 INFO kablam! 272 |         o_buff.write(&real_qual_temp);
Nov 01 17:17:05.425 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.425 INFO kablam!     |
Nov 01 17:17:05.425 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:05.425 INFO kablam! 
Nov 01 17:17:05.426 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:05.426 INFO kablam!    --> src/main.rs:274:5
Nov 01 17:17:05.426 INFO kablam!     |
Nov 01 17:17:05.426 INFO kablam! 274 |     o_buff.write(b"\n");
Nov 01 17:17:05.426 INFO kablam!     |     ^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.426 INFO kablam!     |
Nov 01 17:17:05.426 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:05.426 INFO kablam! 
Nov 01 17:17:05.426 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:05.426 INFO kablam!    --> src/main.rs:277:5
Nov 01 17:17:05.426 INFO kablam!     |
Nov 01 17:17:05.426 INFO kablam! 277 |     o_buff.write(b"\n");
Nov 01 17:17:05.426 INFO kablam!     |     ^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.426 INFO kablam!     |
Nov 01 17:17:05.426 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:05.426 INFO kablam! 
Nov 01 17:17:05.426 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:05.426 INFO kablam!    --> src/main.rs:280:5
Nov 01 17:17:05.426 INFO kablam!     |
Nov 01 17:17:05.426 INFO kablam! 280 |     o_buff.write(b"\n");
Nov 01 17:17:05.426 INFO kablam!     |     ^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.426 INFO kablam!     |
Nov 01 17:17:05.426 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:05.427 INFO kablam! 
Nov 01 17:17:05.427 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Nov 01 17:17:05.427 INFO kablam!    --> src/main.rs:286:10
Nov 01 17:17:05.427 INFO kablam!     |
Nov 01 17:17:05.427 INFO kablam! 286 |     for (key_dupGroup, pair_dup) in pd.iter() {
Nov 01 17:17:05.427 INFO kablam!     |          ^^^^^^^^^^^^
Nov 01 17:17:05.427 INFO kablam! 
Nov 01 17:17:05.427 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group`
Nov 01 17:17:05.427 INFO kablam!    --> src/main.rs:357:9
Nov 01 17:17:05.427 INFO kablam!     |
Nov 01 17:17:05.427 INFO kablam! 357 |     let mut position_dupGroup: HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>> = HashMap::new();
Nov 01 17:17:05.427 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:05.427 INFO kablam! 
Nov 01 17:17:05.427 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Nov 01 17:17:05.427 INFO kablam!    --> src/main.rs:387:17
Nov 01 17:17:05.427 INFO kablam!     |
Nov 01 17:17:05.427 INFO kablam! 387 |             let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size);
Nov 01 17:17:05.427 INFO kablam!     |                 ^^^^^^^^^^^^
Nov 01 17:17:05.427 INFO kablam! 
Nov 01 17:17:08.812 INFO kablam!     Finished dev [unoptimized + debuginfo] target(s) in 39.33s
Nov 01 17:17:08.819 INFO kablam! su: No module specific data is present
Nov 01 17:17:10.584 INFO running `"docker" "rm" "-f" "712394add6a976a87c5a507de288615e3edce4efda255c5f03561ba6f654b276"`
Nov 01 17:17:11.031 INFO blam! 712394add6a976a87c5a507de288615e3edce4efda255c5f03561ba6f654b276
Nov 01 17:17:11.039 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.31-1/worker-7/beta-2018-10-30:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-7/beta-1.31-1/beta-2018-10-30:/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 +beta-2018-10-30 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"`
Nov 01 17:17:11.443 INFO blam! 43b221eb1692e7cb88cd42a2fe8b2212bd1e48a63cc1eb3faca8015ebcdedaac
Nov 01 17:17:11.445 INFO running `"docker" "start" "-a" "43b221eb1692e7cb88cd42a2fe8b2212bd1e48a63cc1eb3faca8015ebcdedaac"`
Nov 01 17:17:13.957 INFO kablam! usermod: no changes
Nov 01 17:17:14.063 INFO kablam!    Compiling consensus v0.1.0 (/source)
Nov 01 17:17:15.403 INFO kablam! warning: unused import: `std::env`
Nov 01 17:17:15.404 INFO kablam!   --> src/main.rs:12:5
Nov 01 17:17:15.405 INFO kablam!    |
Nov 01 17:17:15.405 INFO kablam! 12 | use std::env;
Nov 01 17:17:15.406 INFO kablam!    |     ^^^^^^^^
Nov 01 17:17:15.407 INFO kablam!    |
Nov 01 17:17:15.407 INFO kablam!    = note: #[warn(unused_imports)] on by default
Nov 01 17:17:15.408 INFO kablam! 
Nov 01 17:17:15.409 INFO kablam! warning: unused import: `rust_htslib::prelude::*`
Nov 01 17:17:15.409 INFO kablam!   --> src/main.rs:16:5
Nov 01 17:17:15.410 INFO kablam!    |
Nov 01 17:17:15.410 INFO kablam! 16 | use rust_htslib::prelude::*;
Nov 01 17:17:15.411 INFO kablam!    |     ^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.411 INFO kablam! 
Nov 01 17:17:15.411 INFO kablam! warning: unused import: `std::io`
Nov 01 17:17:15.411 INFO kablam!   --> src/main.rs:21:5
Nov 01 17:17:15.411 INFO kablam!    |
Nov 01 17:17:15.411 INFO kablam! 21 | use std::io;
Nov 01 17:17:15.413 INFO kablam!    |     ^^^^^^^
Nov 01 17:17:15.413 INFO kablam! 
Nov 01 17:17:15.413 INFO kablam! warning: unused import: `PathBuf`
Nov 01 17:17:15.413 INFO kablam!   --> src/main.rs:25:23
Nov 01 17:17:15.413 INFO kablam!    |
Nov 01 17:17:15.413 INFO kablam! 25 | use std::path::{Path, PathBuf};
Nov 01 17:17:15.413 INFO kablam!    |                       ^^^^^^^
Nov 01 17:17:15.414 INFO kablam! 
Nov 01 17:17:15.415 INFO kablam! warning: unused import: `SubCommand`
Nov 01 17:17:15.415 INFO kablam!   --> src/main.rs:26:22
Nov 01 17:17:15.415 INFO kablam!    |
Nov 01 17:17:15.415 INFO kablam! 26 | use clap::{Arg, App, SubCommand};
Nov 01 17:17:15.415 INFO kablam!    |                      ^^^^^^^^^^
Nov 01 17:17:15.415 INFO kablam! 
Nov 01 17:17:15.415 INFO kablam! warning: unnecessary parentheses around `if` condition
Nov 01 17:17:15.415 INFO kablam!    --> src/main.rs:218:20
Nov 01 17:17:15.417 INFO kablam!     |
Nov 01 17:17:15.417 INFO kablam! 218 |                 if (num_position[&(i as usize)] == num_position[&(0 as usize)]) {
Nov 01 17:17:15.417 INFO kablam!     |                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Nov 01 17:17:15.417 INFO kablam!     |
Nov 01 17:17:15.417 INFO kablam!     = note: #[warn(unused_parens)] on by default
Nov 01 17:17:15.417 INFO kablam! 
Nov 01 17:17:15.417 INFO kablam! warning: unnecessary parentheses around `if` condition
Nov 01 17:17:15.417 INFO kablam!    --> src/main.rs:239:16
Nov 01 17:17:15.417 INFO kablam!     |
Nov 01 17:17:15.424 INFO kablam! 239 |             if (baseEach_percent_record.len() > 0) {
Nov 01 17:17:15.424 INFO kablam!     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses
Nov 01 17:17:15.424 INFO kablam! 
Nov 01 17:17:15.599 INFO kablam! warning: unused import: `std::io::prelude`
Nov 01 17:17:15.599 INFO kablam!   --> src/main.rs:22:5
Nov 01 17:17:15.599 INFO kablam!    |
Nov 01 17:17:15.599 INFO kablam! 22 | use std::io::prelude::*;
Nov 01 17:17:15.599 INFO kablam!    |     ^^^^^^^^^^^^^^^^
Nov 01 17:17:15.599 INFO kablam! 
Nov 01 17:17:15.612 INFO kablam! warning: unused variable: `consensus_base`
Nov 01 17:17:15.612 INFO kablam!    --> src/main.rs:139:9
Nov 01 17:17:15.612 INFO kablam!     |
Nov 01 17:17:15.612 INFO kablam! 139 |     let consensus_base:Vec<u8> = Vec::new();
Nov 01 17:17:15.612 INFO kablam!     |         ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead
Nov 01 17:17:15.612 INFO kablam!     |
Nov 01 17:17:15.612 INFO kablam!     = note: #[warn(unused_variables)] on by default
Nov 01 17:17:15.612 INFO kablam! 
Nov 01 17:17:15.612 INFO kablam! warning: unused variable: `consensus_source_reads`
Nov 01 17:17:15.612 INFO kablam!    --> src/main.rs:144:13
Nov 01 17:17:15.612 INFO kablam!     |
Nov 01 17:17:15.612 INFO kablam! 144 |     let mut consensus_source_reads = String::new();
Nov 01 17:17:15.612 INFO kablam!     |             ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead
Nov 01 17:17:15.612 INFO kablam! 
Nov 01 17:17:15.612 INFO kablam! warning: unused variable: `chrom`
Nov 01 17:17:15.612 INFO kablam!    --> src/main.rs:283:121
Nov 01 17:17:15.612 INFO kablam!     |
Nov 01 17:17:15.612 INFO kablam! 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 01 17:17:15.613 INFO kablam!     |                                                                                                                         ^^^^^ help: consider using `_chrom` instead
Nov 01 17:17:15.613 INFO kablam! 
Nov 01 17:17:15.613 INFO kablam! warning: value assigned to `new_seq_b` is never read
Nov 01 17:17:15.613 INFO kablam!    --> src/main.rs:370:21
Nov 01 17:17:15.613 INFO kablam!     |
Nov 01 17:17:15.613 INFO kablam! 370 |             let mut new_seq_b:Vec<u8> = Vec::new();
Nov 01 17:17:15.613 INFO kablam!     |                     ^^^^^^^^^
Nov 01 17:17:15.613 INFO kablam!     |
Nov 01 17:17:15.613 INFO kablam!     = note: #[warn(unused_assignments)] on by default
Nov 01 17:17:15.613 INFO kablam! 
Nov 01 17:17:15.626 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:15.626 INFO kablam!   --> src/main.rs:74:9
Nov 01 17:17:15.626 INFO kablam!    |
Nov 01 17:17:15.626 INFO kablam! 74 |     let mut pair;
Nov 01 17:17:15.626 INFO kablam!    |         ----^^^^
Nov 01 17:17:15.626 INFO kablam!    |         |
Nov 01 17:17:15.626 INFO kablam!    |         help: remove this `mut`
Nov 01 17:17:15.626 INFO kablam!    |
Nov 01 17:17:15.626 INFO kablam!    = note: #[warn(unused_mut)] on by default
Nov 01 17:17:15.626 INFO kablam! 
Nov 01 17:17:15.627 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:15.627 INFO kablam!   --> src/main.rs:75:9
Nov 01 17:17:15.627 INFO kablam!    |
Nov 01 17:17:15.627 INFO kablam! 75 |     let mut strand;
Nov 01 17:17:15.627 INFO kablam!    |         ----^^^^^^
Nov 01 17:17:15.627 INFO kablam!    |         |
Nov 01 17:17:15.627 INFO kablam!    |         help: remove this `mut`
Nov 01 17:17:15.627 INFO kablam! 
Nov 01 17:17:15.627 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:15.627 INFO kablam!   --> src/main.rs:76:9
Nov 01 17:17:15.627 INFO kablam!    |
Nov 01 17:17:15.627 INFO kablam! 76 |     let mut aln_pos;
Nov 01 17:17:15.627 INFO kablam!    |         ----^^^^^^^
Nov 01 17:17:15.627 INFO kablam!    |         |
Nov 01 17:17:15.627 INFO kablam!    |         help: remove this `mut`
Nov 01 17:17:15.627 INFO kablam! 
Nov 01 17:17:15.667 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:15.667 INFO kablam!    --> src/main.rs:144:9
Nov 01 17:17:15.667 INFO kablam!     |
Nov 01 17:17:15.667 INFO kablam! 144 |     let mut consensus_source_reads = String::new();
Nov 01 17:17:15.667 INFO kablam!     |         ----^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.667 INFO kablam!     |         |
Nov 01 17:17:15.667 INFO kablam!     |         help: remove this `mut`
Nov 01 17:17:15.667 INFO kablam! 
Nov 01 17:17:15.667 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:15.667 INFO kablam!    --> src/main.rs:151:9
Nov 01 17:17:15.667 INFO kablam!     |
Nov 01 17:17:15.667 INFO kablam! 151 |     let mut top_cigar:&CigarStringView;
Nov 01 17:17:15.667 INFO kablam!     |         ----^^^^^^^^^
Nov 01 17:17:15.667 INFO kablam!     |         |
Nov 01 17:17:15.667 INFO kablam!     |         help: remove this `mut`
Nov 01 17:17:15.667 INFO kablam! 
Nov 01 17:17:15.683 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:15.683 INFO kablam!    --> src/main.rs:338:9
Nov 01 17:17:15.683 INFO kablam!     |
Nov 01 17:17:15.683 INFO kablam! 338 |     let mut need_trim:bool;
Nov 01 17:17:15.683 INFO kablam!     |         ----^^^^^^^^^
Nov 01 17:17:15.683 INFO kablam!     |         |
Nov 01 17:17:15.683 INFO kablam!     |         help: remove this `mut`
Nov 01 17:17:15.683 INFO kablam! 
Nov 01 17:17:15.683 INFO kablam! warning: variable does not need to be mutable
Nov 01 17:17:15.683 INFO kablam!    --> src/main.rs:355:9
Nov 01 17:17:15.683 INFO kablam!     |
Nov 01 17:17:15.683 INFO kablam! 355 |     let mut chrom = 0;
Nov 01 17:17:15.683 INFO kablam!     |         ----^^^^^
Nov 01 17:17:15.683 INFO kablam!     |         |
Nov 01 17:17:15.683 INFO kablam!     |         help: remove this `mut`
Nov 01 17:17:15.683 INFO kablam! 
Nov 01 17:17:15.698 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse`
Nov 01 17:17:15.698 INFO kablam!   --> src/main.rs:68:1
Nov 01 17:17:15.698 INFO kablam!    |
Nov 01 17:17:15.698 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){
Nov 01 17:17:15.698 INFO kablam! 69 | |
Nov 01 17:17:15.698 INFO kablam! 70 | |     let qname_str = String::from_utf8_lossy(record.qname()).to_string();
Nov 01 17:17:15.698 INFO kablam! 71 | |     let temp_v:Vec<&str> = qname_str.split('#').collect();
Nov 01 17:17:15.698 INFO kablam! ...  |
Nov 01 17:17:15.698 INFO kablam! 97 | |     (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos)
Nov 01 17:17:15.698 INFO kablam! 98 | | }
Nov 01 17:17:15.698 INFO kablam!    | |_^
Nov 01 17:17:15.698 INFO kablam!    |
Nov 01 17:17:15.698 INFO kablam!    = note: #[warn(non_snake_case)] on by default
Nov 01 17:17:15.698 INFO kablam! 
Nov 01 17:17:15.703 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record`
Nov 01 17:17:15.703 INFO kablam!    --> src/main.rs:147:9
Nov 01 17:17:15.703 INFO kablam!     |
Nov 01 17:17:15.703 INFO kablam! 147 |     let mut baseEach_num_record = String::new();
Nov 01 17:17:15.703 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.703 INFO kablam! 
Nov 01 17:17:15.703 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record`
Nov 01 17:17:15.703 INFO kablam!    --> src/main.rs:148:9
Nov 01 17:17:15.703 INFO kablam!     |
Nov 01 17:17:15.703 INFO kablam! 148 |     let mut baseEach_percent_record = String::new();
Nov 01 17:17:15.703 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.704 INFO kablam! 
Nov 01 17:17:15.704 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:15.704 INFO kablam!    --> src/main.rs:267:9
Nov 01 17:17:15.704 INFO kablam!     |
Nov 01 17:17:15.704 INFO kablam! 267 |         o_buff.write(&member_record.2);
Nov 01 17:17:15.704 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.704 INFO kablam!     |
Nov 01 17:17:15.704 INFO kablam!     = note: #[warn(unused_must_use)] on by default
Nov 01 17:17:15.704 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:15.704 INFO kablam! 
Nov 01 17:17:15.704 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:15.704 INFO kablam!    --> src/main.rs:269:9
Nov 01 17:17:15.704 INFO kablam!     |
Nov 01 17:17:15.704 INFO kablam! 269 |         o_buff.write(&member_record.0);
Nov 01 17:17:15.704 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.704 INFO kablam!     |
Nov 01 17:17:15.704 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:15.705 INFO kablam! 
Nov 01 17:17:15.705 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:15.705 INFO kablam!    --> src/main.rs:272:9
Nov 01 17:17:15.705 INFO kablam!     |
Nov 01 17:17:15.705 INFO kablam! 272 |         o_buff.write(&real_qual_temp);
Nov 01 17:17:15.705 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.705 INFO kablam!     |
Nov 01 17:17:15.705 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:15.705 INFO kablam! 
Nov 01 17:17:15.705 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:15.705 INFO kablam!    --> src/main.rs:274:5
Nov 01 17:17:15.705 INFO kablam!     |
Nov 01 17:17:15.705 INFO kablam! 274 |     o_buff.write(b"\n");
Nov 01 17:17:15.706 INFO kablam!     |     ^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.706 INFO kablam!     |
Nov 01 17:17:15.706 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:15.706 INFO kablam! 
Nov 01 17:17:15.706 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:15.706 INFO kablam!    --> src/main.rs:277:5
Nov 01 17:17:15.706 INFO kablam!     |
Nov 01 17:17:15.706 INFO kablam! 277 |     o_buff.write(b"\n");
Nov 01 17:17:15.706 INFO kablam!     |     ^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.706 INFO kablam!     |
Nov 01 17:17:15.706 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:15.706 INFO kablam! 
Nov 01 17:17:15.706 INFO kablam! warning: unused `std::result::Result` that must be used
Nov 01 17:17:15.706 INFO kablam!    --> src/main.rs:280:5
Nov 01 17:17:15.706 INFO kablam!     |
Nov 01 17:17:15.706 INFO kablam! 280 |     o_buff.write(b"\n");
Nov 01 17:17:15.706 INFO kablam!     |     ^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.706 INFO kablam!     |
Nov 01 17:17:15.706 INFO kablam!     = note: this `Result` may be an `Err` variant, which should be handled
Nov 01 17:17:15.706 INFO kablam! 
Nov 01 17:17:15.706 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Nov 01 17:17:15.706 INFO kablam!    --> src/main.rs:286:10
Nov 01 17:17:15.706 INFO kablam!     |
Nov 01 17:17:15.706 INFO kablam! 286 |     for (key_dupGroup, pair_dup) in pd.iter() {
Nov 01 17:17:15.706 INFO kablam!     |          ^^^^^^^^^^^^
Nov 01 17:17:15.706 INFO kablam! 
Nov 01 17:17:15.715 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group`
Nov 01 17:17:15.715 INFO kablam!    --> src/main.rs:357:9
Nov 01 17:17:15.715 INFO kablam!     |
Nov 01 17:17:15.715 INFO kablam! 357 |     let mut position_dupGroup: HashMap<String, HashMap<String, Vec<(Vec<u8>, Vec<u8>, Vec<u8>, CigarStringView, bool)>>> = HashMap::new();
Nov 01 17:17:15.715 INFO kablam!     |         ^^^^^^^^^^^^^^^^^^^^^
Nov 01 17:17:15.715 INFO kablam! 
Nov 01 17:17:15.715 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group`
Nov 01 17:17:15.715 INFO kablam!    --> src/main.rs:387:17
Nov 01 17:17:15.715 INFO kablam!     |
Nov 01 17:17:15.715 INFO kablam! 387 |             let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size);
Nov 01 17:17:15.715 INFO kablam!     |                 ^^^^^^^^^^^^
Nov 01 17:17:15.715 INFO kablam! 
Nov 01 17:17:16.361 INFO kablam!     Finished dev [unoptimized + debuginfo] target(s) in 2.38s
Nov 01 17:17:16.387 INFO kablam! su: No module specific data is present
Nov 01 17:17:17.305 INFO running `"docker" "rm" "-f" "43b221eb1692e7cb88cd42a2fe8b2212bd1e48a63cc1eb3faca8015ebcdedaac"`
Nov 01 17:17:17.655 INFO blam! 43b221eb1692e7cb88cd42a2fe8b2212bd1e48a63cc1eb3faca8015ebcdedaac
Nov 01 17:17:17.664 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.31-1/worker-7/beta-2018-10-30:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-7/beta-1.31-1/beta-2018-10-30:/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 +beta-2018-10-30 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"`
Nov 01 17:17:18.180 INFO blam! d6a2e50ec45c26c7138c655b75e27294563a84a486ee6ca056eca2b959311601
Nov 01 17:17:18.195 INFO running `"docker" "start" "-a" "d6a2e50ec45c26c7138c655b75e27294563a84a486ee6ca056eca2b959311601"`
Nov 01 17:17:20.137 INFO kablam! usermod: no changes
Nov 01 17:17:20.298 INFO kablam!     Finished dev [unoptimized + debuginfo] target(s) in 0.12s
Nov 01 17:17:20.310 INFO kablam!      Running /target/debug/deps/consensus-205c90f31f5e90d9
Nov 01 17:17:20.328 INFO blam! 
Nov 01 17:17:20.328 INFO blam! running 0 tests
Nov 01 17:17:20.329 INFO blam! 
Nov 01 17:17:20.329 INFO blam! test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out
Nov 01 17:17:20.329 INFO blam! 
Nov 01 17:17:20.339 INFO kablam! su: No module specific data is present
Nov 01 17:17:22.087 INFO running `"docker" "rm" "-f" "d6a2e50ec45c26c7138c655b75e27294563a84a486ee6ca056eca2b959311601"`
Nov 01 17:17:22.508 INFO blam! d6a2e50ec45c26c7138c655b75e27294563a84a486ee6ca056eca2b959311601
