Aug 29 20:46:57.232 INFO checking TuBieJun/consensus against try#2d477f9981361618ac78253c28051a66b6cea125 for pr-53707 Aug 29 20:46:57.232 INFO running: cargo +2d477f9981361618ac78253c28051a66b6cea125-alt check --frozen --all --all-targets Aug 29 20:46:57.232 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-1/pr-53707/try#2d477f9981361618ac78253c28051a66b6cea125:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-53707/worker-1/try#2d477f9981361618ac78253c28051a66b6cea125:/target:rw,Z" "-v" "/home/ec2-user/crater/./work/local/cargo-home:/cargo-home:ro,Z" "-v" "/home/ec2-user/crater/./work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=500" "-e" "CMD=cargo +2d477f9981361618ac78253c28051a66b6cea125-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "2G" "crater"` Aug 29 20:46:57.460 INFO blam! 9c18a4432fa0345184d826a11bee3684bae6936231f9bf744b02602eb780689d Aug 29 20:46:57.460 INFO running `"docker" "start" "-a" "9c18a4432fa0345184d826a11bee3684bae6936231f9bf744b02602eb780689d"` Aug 29 20:46:58.423 INFO kablam! Checking ieee754 v0.2.2 Aug 29 20:46:58.428 INFO kablam! Compiling fs-utils v1.0.0 Aug 29 20:46:58.429 INFO kablam! Checking itertools v0.6.5 Aug 29 20:46:58.429 INFO kablam! Checking atty v0.2.6 Aug 29 20:46:59.043 INFO kablam! Checking clap v2.29.0 Aug 29 20:47:00.141 INFO kablam! Compiling rust-htslib v0.15.0 Aug 29 20:47:40.664 INFO kablam! Checking consensus v0.1.0 (file:///source) Aug 29 20:47:41.388 INFO kablam! warning: unused import: `std::env` Aug 29 20:47:41.388 INFO kablam! --> src/main.rs:12:5 Aug 29 20:47:41.388 INFO kablam! | Aug 29 20:47:41.388 INFO kablam! 12 | use std::env; Aug 29 20:47:41.388 INFO kablam! | ^^^^^^^^ Aug 29 20:47:41.388 INFO kablam! | Aug 29 20:47:41.388 INFO kablam! = note: #[warn(unused_imports)] on by default Aug 29 20:47:41.389 INFO kablam! Aug 29 20:47:41.389 INFO kablam! warning: unused import: `rust_htslib::prelude::*` Aug 29 20:47:41.389 INFO kablam! --> src/main.rs:16:5 Aug 29 20:47:41.389 INFO kablam! | Aug 29 20:47:41.389 INFO kablam! 16 | use rust_htslib::prelude::*; Aug 29 20:47:41.389 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.389 INFO kablam! Aug 29 20:47:41.389 INFO kablam! warning: unused import: `std::io` Aug 29 20:47:41.389 INFO kablam! --> src/main.rs:21:5 Aug 29 20:47:41.389 INFO kablam! | Aug 29 20:47:41.390 INFO kablam! 21 | use std::io; Aug 29 20:47:41.390 INFO kablam! | ^^^^^^^ Aug 29 20:47:41.390 INFO kablam! Aug 29 20:47:41.390 INFO kablam! warning: unused import: `PathBuf` Aug 29 20:47:41.390 INFO kablam! --> src/main.rs:25:23 Aug 29 20:47:41.390 INFO kablam! | Aug 29 20:47:41.390 INFO kablam! 25 | use std::path::{Path, PathBuf}; Aug 29 20:47:41.390 INFO kablam! | ^^^^^^^ Aug 29 20:47:41.390 INFO kablam! Aug 29 20:47:41.390 INFO kablam! warning: unused import: `SubCommand` Aug 29 20:47:41.390 INFO kablam! --> src/main.rs:26:22 Aug 29 20:47:41.390 INFO kablam! | Aug 29 20:47:41.390 INFO kablam! 26 | use clap::{Arg, App, SubCommand}; Aug 29 20:47:41.390 INFO kablam! | ^^^^^^^^^^ Aug 29 20:47:41.390 INFO kablam! Aug 29 20:47:41.390 INFO kablam! warning: unnecessary parentheses around `if` condition Aug 29 20:47:41.390 INFO kablam! --> src/main.rs:218:20 Aug 29 20:47:41.390 INFO kablam! | Aug 29 20:47:41.390 INFO kablam! 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Aug 29 20:47:41.390 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Aug 29 20:47:41.390 INFO kablam! | Aug 29 20:47:41.391 INFO kablam! = note: #[warn(unused_parens)] on by default Aug 29 20:47:41.391 INFO kablam! Aug 29 20:47:41.391 INFO kablam! warning: unnecessary parentheses around `if` condition Aug 29 20:47:41.391 INFO kablam! --> src/main.rs:239:16 Aug 29 20:47:41.391 INFO kablam! | Aug 29 20:47:41.391 INFO kablam! 239 | if (baseEach_percent_record.len() > 0) { Aug 29 20:47:41.391 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Aug 29 20:47:41.391 INFO kablam! Aug 29 20:47:41.568 INFO kablam! warning: unused import: `std::env` Aug 29 20:47:41.568 INFO kablam! --> src/main.rs:12:5 Aug 29 20:47:41.568 INFO kablam! | Aug 29 20:47:41.568 INFO kablam! 12 | use std::env; Aug 29 20:47:41.568 INFO kablam! | ^^^^^^^^ Aug 29 20:47:41.569 INFO kablam! | Aug 29 20:47:41.569 INFO kablam! = note: #[warn(unused_imports)] on by default Aug 29 20:47:41.569 INFO kablam! Aug 29 20:47:41.569 INFO kablam! warning: unused import: `rust_htslib::prelude::*` Aug 29 20:47:41.569 INFO kablam! --> src/main.rs:16:5 Aug 29 20:47:41.569 INFO kablam! | Aug 29 20:47:41.569 INFO kablam! 16 | use rust_htslib::prelude::*; Aug 29 20:47:41.569 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.572 INFO kablam! Aug 29 20:47:41.573 INFO kablam! warning: unused import: `std::io` Aug 29 20:47:41.573 INFO kablam! --> src/main.rs:21:5 Aug 29 20:47:41.573 INFO kablam! | Aug 29 20:47:41.573 INFO kablam! 21 | use std::io; Aug 29 20:47:41.573 INFO kablam! | ^^^^^^^ Aug 29 20:47:41.573 INFO kablam! Aug 29 20:47:41.573 INFO kablam! warning: unused import: `PathBuf` Aug 29 20:47:41.573 INFO kablam! --> src/main.rs:25:23 Aug 29 20:47:41.573 INFO kablam! | Aug 29 20:47:41.573 INFO kablam! 25 | use std::path::{Path, PathBuf}; Aug 29 20:47:41.573 INFO kablam! | ^^^^^^^ Aug 29 20:47:41.573 INFO kablam! Aug 29 20:47:41.573 INFO kablam! warning: unused import: `SubCommand` Aug 29 20:47:41.573 INFO kablam! --> src/main.rs:26:22 Aug 29 20:47:41.573 INFO kablam! | Aug 29 20:47:41.573 INFO kablam! 26 | use clap::{Arg, App, SubCommand}; Aug 29 20:47:41.573 INFO kablam! | ^^^^^^^^^^ Aug 29 20:47:41.573 INFO kablam! Aug 29 20:47:41.574 INFO kablam! warning: unnecessary parentheses around `if` condition Aug 29 20:47:41.574 INFO kablam! --> src/main.rs:218:20 Aug 29 20:47:41.574 INFO kablam! | Aug 29 20:47:41.574 INFO kablam! 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Aug 29 20:47:41.574 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Aug 29 20:47:41.574 INFO kablam! | Aug 29 20:47:41.574 INFO kablam! = note: #[warn(unused_parens)] on by default Aug 29 20:47:41.574 INFO kablam! Aug 29 20:47:41.574 INFO kablam! warning: unnecessary parentheses around `if` condition Aug 29 20:47:41.574 INFO kablam! --> src/main.rs:239:16 Aug 29 20:47:41.574 INFO kablam! | Aug 29 20:47:41.574 INFO kablam! 239 | if (baseEach_percent_record.len() > 0) { Aug 29 20:47:41.574 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Aug 29 20:47:41.574 INFO kablam! Aug 29 20:47:41.713 INFO kablam! warning: unused import: `std::io::prelude` Aug 29 20:47:41.713 INFO kablam! --> src/main.rs:22:5 Aug 29 20:47:41.713 INFO kablam! | Aug 29 20:47:41.713 INFO kablam! 22 | use std::io::prelude::*; Aug 29 20:47:41.713 INFO kablam! | ^^^^^^^^^^^^^^^^ Aug 29 20:47:41.713 INFO kablam! Aug 29 20:47:41.774 INFO kablam! warning: unused variable: `consensus_base` Aug 29 20:47:41.774 INFO kablam! --> src/main.rs:139:9 Aug 29 20:47:41.774 INFO kablam! | Aug 29 20:47:41.774 INFO kablam! 139 | let consensus_base:Vec = Vec::new(); Aug 29 20:47:41.774 INFO kablam! | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Aug 29 20:47:41.774 INFO kablam! | Aug 29 20:47:41.774 INFO kablam! = note: #[warn(unused_variables)] on by default Aug 29 20:47:41.774 INFO kablam! Aug 29 20:47:41.775 INFO kablam! warning: unused variable: `consensus_source_reads` Aug 29 20:47:41.775 INFO kablam! --> src/main.rs:144:13 Aug 29 20:47:41.775 INFO kablam! | Aug 29 20:47:41.775 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Aug 29 20:47:41.775 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Aug 29 20:47:41.775 INFO kablam! Aug 29 20:47:41.775 INFO kablam! warning: unused variable: `chrom` Aug 29 20:47:41.775 INFO kablam! --> src/main.rs:283:121 Aug 29 20:47:41.775 INFO kablam! | Aug 29 20:47:41.775 INFO kablam! 283 | fn block_consensus(pd:& mut HashMap, Vec, Vec, CigarStringView, bool)>>>, chrom: i32, use_check:bool, min_t_s: &u32, min_t_p: &f32, o_r1: & mut File, o_r2: & mut File, need_trim:bool) { Aug 29 20:47:41.775 INFO kablam! | ^^^^^ help: consider using `_chrom` instead Aug 29 20:47:41.775 INFO kablam! Aug 29 20:47:41.775 INFO kablam! warning: value assigned to `new_seq_b` is never read Aug 29 20:47:41.775 INFO kablam! --> src/main.rs:370:21 Aug 29 20:47:41.775 INFO kablam! | Aug 29 20:47:41.776 INFO kablam! 370 | let mut new_seq_b:Vec = Vec::new(); Aug 29 20:47:41.776 INFO kablam! | ^^^^^^^^^ Aug 29 20:47:41.776 INFO kablam! | Aug 29 20:47:41.776 INFO kablam! = note: #[warn(unused_assignments)] on by default Aug 29 20:47:41.776 INFO kablam! Aug 29 20:47:41.788 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.788 INFO kablam! --> src/main.rs:74:9 Aug 29 20:47:41.788 INFO kablam! | Aug 29 20:47:41.788 INFO kablam! 74 | let mut pair; Aug 29 20:47:41.788 INFO kablam! | ----^^^^ Aug 29 20:47:41.788 INFO kablam! | | Aug 29 20:47:41.788 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.788 INFO kablam! | Aug 29 20:47:41.788 INFO kablam! = note: #[warn(unused_mut)] on by default Aug 29 20:47:41.788 INFO kablam! Aug 29 20:47:41.789 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.789 INFO kablam! --> src/main.rs:75:9 Aug 29 20:47:41.789 INFO kablam! | Aug 29 20:47:41.789 INFO kablam! 75 | let mut strand; Aug 29 20:47:41.789 INFO kablam! | ----^^^^^^ Aug 29 20:47:41.789 INFO kablam! | | Aug 29 20:47:41.789 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.789 INFO kablam! Aug 29 20:47:41.789 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.789 INFO kablam! --> src/main.rs:76:9 Aug 29 20:47:41.789 INFO kablam! | Aug 29 20:47:41.789 INFO kablam! 76 | let mut aln_pos; Aug 29 20:47:41.789 INFO kablam! | ----^^^^^^^ Aug 29 20:47:41.789 INFO kablam! | | Aug 29 20:47:41.789 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.789 INFO kablam! Aug 29 20:47:41.844 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.847 INFO kablam! --> src/main.rs:144:9 Aug 29 20:47:41.847 INFO kablam! | Aug 29 20:47:41.847 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Aug 29 20:47:41.847 INFO kablam! | ----^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.847 INFO kablam! | | Aug 29 20:47:41.847 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.847 INFO kablam! Aug 29 20:47:41.847 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.847 INFO kablam! --> src/main.rs:151:9 Aug 29 20:47:41.847 INFO kablam! | Aug 29 20:47:41.847 INFO kablam! 151 | let mut top_cigar:&CigarStringView; Aug 29 20:47:41.847 INFO kablam! | ----^^^^^^^^^ Aug 29 20:47:41.847 INFO kablam! | | Aug 29 20:47:41.847 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.847 INFO kablam! Aug 29 20:47:41.874 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.875 INFO kablam! --> src/main.rs:338:9 Aug 29 20:47:41.875 INFO kablam! | Aug 29 20:47:41.875 INFO kablam! 338 | let mut need_trim:bool; Aug 29 20:47:41.875 INFO kablam! | ----^^^^^^^^^ Aug 29 20:47:41.875 INFO kablam! | | Aug 29 20:47:41.875 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.875 INFO kablam! Aug 29 20:47:41.875 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.875 INFO kablam! --> src/main.rs:355:9 Aug 29 20:47:41.875 INFO kablam! | Aug 29 20:47:41.875 INFO kablam! 355 | let mut chrom = 0; Aug 29 20:47:41.875 INFO kablam! | ----^^^^^ Aug 29 20:47:41.875 INFO kablam! | | Aug 29 20:47:41.875 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.875 INFO kablam! Aug 29 20:47:41.877 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Aug 29 20:47:41.877 INFO kablam! --> src/main.rs:68:1 Aug 29 20:47:41.877 INFO kablam! | Aug 29 20:47:41.877 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Aug 29 20:47:41.877 INFO kablam! 69 | | Aug 29 20:47:41.877 INFO kablam! 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Aug 29 20:47:41.877 INFO kablam! 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Aug 29 20:47:41.877 INFO kablam! ... | Aug 29 20:47:41.877 INFO kablam! 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Aug 29 20:47:41.877 INFO kablam! 98 | | } Aug 29 20:47:41.877 INFO kablam! | |_^ Aug 29 20:47:41.877 INFO kablam! | Aug 29 20:47:41.877 INFO kablam! = note: #[warn(non_snake_case)] on by default Aug 29 20:47:41.877 INFO kablam! Aug 29 20:47:41.878 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Aug 29 20:47:41.878 INFO kablam! --> src/main.rs:147:9 Aug 29 20:47:41.878 INFO kablam! | Aug 29 20:47:41.878 INFO kablam! 147 | let mut baseEach_num_record = String::new(); Aug 29 20:47:41.878 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.878 INFO kablam! Aug 29 20:47:41.878 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Aug 29 20:47:41.878 INFO kablam! --> src/main.rs:148:9 Aug 29 20:47:41.878 INFO kablam! | Aug 29 20:47:41.878 INFO kablam! 148 | let mut baseEach_percent_record = String::new(); Aug 29 20:47:41.878 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.878 INFO kablam! Aug 29 20:47:41.878 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:41.878 INFO kablam! --> src/main.rs:267:9 Aug 29 20:47:41.878 INFO kablam! | Aug 29 20:47:41.878 INFO kablam! 267 | o_buff.write(&member_record.2); Aug 29 20:47:41.879 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.879 INFO kablam! | Aug 29 20:47:41.879 INFO kablam! = note: #[warn(unused_must_use)] on by default Aug 29 20:47:41.879 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:41.879 INFO kablam! Aug 29 20:47:41.879 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:41.879 INFO kablam! --> src/main.rs:269:9 Aug 29 20:47:41.879 INFO kablam! | Aug 29 20:47:41.879 INFO kablam! 269 | o_buff.write(&member_record.0); Aug 29 20:47:41.880 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.880 INFO kablam! | Aug 29 20:47:41.880 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:41.880 INFO kablam! Aug 29 20:47:41.880 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:41.880 INFO kablam! --> src/main.rs:272:9 Aug 29 20:47:41.880 INFO kablam! | Aug 29 20:47:41.880 INFO kablam! 272 | o_buff.write(&real_qual_temp); Aug 29 20:47:41.880 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.880 INFO kablam! | Aug 29 20:47:41.880 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:41.880 INFO kablam! Aug 29 20:47:41.881 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:41.881 INFO kablam! --> src/main.rs:274:5 Aug 29 20:47:41.881 INFO kablam! | Aug 29 20:47:41.881 INFO kablam! 274 | o_buff.write(b"\n"); Aug 29 20:47:41.881 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.881 INFO kablam! | Aug 29 20:47:41.881 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:41.881 INFO kablam! Aug 29 20:47:41.881 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:41.881 INFO kablam! --> src/main.rs:277:5 Aug 29 20:47:41.881 INFO kablam! | Aug 29 20:47:41.881 INFO kablam! 277 | o_buff.write(b"\n"); Aug 29 20:47:41.881 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.881 INFO kablam! | Aug 29 20:47:41.881 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:41.881 INFO kablam! Aug 29 20:47:41.882 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:41.882 INFO kablam! --> src/main.rs:280:5 Aug 29 20:47:41.882 INFO kablam! | Aug 29 20:47:41.882 INFO kablam! 280 | o_buff.write(b"\n"); Aug 29 20:47:41.882 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.882 INFO kablam! | Aug 29 20:47:41.882 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:41.882 INFO kablam! Aug 29 20:47:41.882 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Aug 29 20:47:41.882 INFO kablam! --> src/main.rs:286:10 Aug 29 20:47:41.882 INFO kablam! | Aug 29 20:47:41.882 INFO kablam! 286 | for (key_dupGroup, pair_dup) in pd.iter() { Aug 29 20:47:41.882 INFO kablam! | ^^^^^^^^^^^^ Aug 29 20:47:41.882 INFO kablam! Aug 29 20:47:41.883 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Aug 29 20:47:41.883 INFO kablam! --> src/main.rs:357:9 Aug 29 20:47:41.883 INFO kablam! | Aug 29 20:47:41.883 INFO kablam! 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Aug 29 20:47:41.883 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:41.883 INFO kablam! Aug 29 20:47:41.883 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Aug 29 20:47:41.884 INFO kablam! --> src/main.rs:387:17 Aug 29 20:47:41.884 INFO kablam! | Aug 29 20:47:41.884 INFO kablam! 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Aug 29 20:47:41.884 INFO kablam! | ^^^^^^^^^^^^ Aug 29 20:47:41.884 INFO kablam! Aug 29 20:47:41.909 INFO kablam! warning: unused import: `std::io::prelude` Aug 29 20:47:41.909 INFO kablam! --> src/main.rs:22:5 Aug 29 20:47:41.909 INFO kablam! | Aug 29 20:47:41.909 INFO kablam! 22 | use std::io::prelude::*; Aug 29 20:47:41.909 INFO kablam! | ^^^^^^^^^^^^^^^^ Aug 29 20:47:41.909 INFO kablam! Aug 29 20:47:41.979 INFO kablam! warning: unused variable: `consensus_base` Aug 29 20:47:41.979 INFO kablam! --> src/main.rs:139:9 Aug 29 20:47:41.979 INFO kablam! | Aug 29 20:47:41.979 INFO kablam! 139 | let consensus_base:Vec = Vec::new(); Aug 29 20:47:41.979 INFO kablam! | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Aug 29 20:47:41.979 INFO kablam! | Aug 29 20:47:41.979 INFO kablam! = note: #[warn(unused_variables)] on by default Aug 29 20:47:41.979 INFO kablam! Aug 29 20:47:41.979 INFO kablam! warning: unused variable: `consensus_source_reads` Aug 29 20:47:41.979 INFO kablam! --> src/main.rs:144:13 Aug 29 20:47:41.979 INFO kablam! | Aug 29 20:47:41.979 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Aug 29 20:47:41.979 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Aug 29 20:47:41.979 INFO kablam! Aug 29 20:47:41.979 INFO kablam! warning: unused variable: `chrom` Aug 29 20:47:41.979 INFO kablam! --> src/main.rs:283:121 Aug 29 20:47:41.980 INFO kablam! | Aug 29 20:47:41.980 INFO kablam! 283 | fn block_consensus(pd:& mut HashMap, Vec, Vec, CigarStringView, bool)>>>, chrom: i32, use_check:bool, min_t_s: &u32, min_t_p: &f32, o_r1: & mut File, o_r2: & mut File, need_trim:bool) { Aug 29 20:47:41.980 INFO kablam! | ^^^^^ help: consider using `_chrom` instead Aug 29 20:47:41.980 INFO kablam! Aug 29 20:47:41.980 INFO kablam! warning: value assigned to `new_seq_b` is never read Aug 29 20:47:41.980 INFO kablam! --> src/main.rs:370:21 Aug 29 20:47:41.980 INFO kablam! | Aug 29 20:47:41.980 INFO kablam! 370 | let mut new_seq_b:Vec = Vec::new(); Aug 29 20:47:41.980 INFO kablam! | ^^^^^^^^^ Aug 29 20:47:41.980 INFO kablam! | Aug 29 20:47:41.980 INFO kablam! = note: #[warn(unused_assignments)] on by default Aug 29 20:47:41.980 INFO kablam! Aug 29 20:47:41.994 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.994 INFO kablam! --> src/main.rs:74:9 Aug 29 20:47:41.994 INFO kablam! | Aug 29 20:47:41.994 INFO kablam! 74 | let mut pair; Aug 29 20:47:41.994 INFO kablam! | ----^^^^ Aug 29 20:47:41.994 INFO kablam! | | Aug 29 20:47:41.994 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.994 INFO kablam! | Aug 29 20:47:41.994 INFO kablam! = note: #[warn(unused_mut)] on by default Aug 29 20:47:41.994 INFO kablam! Aug 29 20:47:41.994 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.994 INFO kablam! --> src/main.rs:75:9 Aug 29 20:47:41.994 INFO kablam! | Aug 29 20:47:41.995 INFO kablam! 75 | let mut strand; Aug 29 20:47:41.995 INFO kablam! | ----^^^^^^ Aug 29 20:47:41.995 INFO kablam! | | Aug 29 20:47:41.995 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.995 INFO kablam! Aug 29 20:47:41.995 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:41.995 INFO kablam! --> src/main.rs:76:9 Aug 29 20:47:41.995 INFO kablam! | Aug 29 20:47:41.995 INFO kablam! 76 | let mut aln_pos; Aug 29 20:47:41.995 INFO kablam! | ----^^^^^^^ Aug 29 20:47:41.995 INFO kablam! | | Aug 29 20:47:41.995 INFO kablam! | help: remove this `mut` Aug 29 20:47:41.995 INFO kablam! Aug 29 20:47:42.052 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:42.052 INFO kablam! --> src/main.rs:144:9 Aug 29 20:47:42.053 INFO kablam! | Aug 29 20:47:42.053 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Aug 29 20:47:42.053 INFO kablam! | ----^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.053 INFO kablam! | | Aug 29 20:47:42.053 INFO kablam! | help: remove this `mut` Aug 29 20:47:42.053 INFO kablam! Aug 29 20:47:42.053 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:42.053 INFO kablam! --> src/main.rs:151:9 Aug 29 20:47:42.053 INFO kablam! | Aug 29 20:47:42.053 INFO kablam! 151 | let mut top_cigar:&CigarStringView; Aug 29 20:47:42.053 INFO kablam! | ----^^^^^^^^^ Aug 29 20:47:42.053 INFO kablam! | | Aug 29 20:47:42.053 INFO kablam! | help: remove this `mut` Aug 29 20:47:42.053 INFO kablam! Aug 29 20:47:42.082 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:42.082 INFO kablam! --> src/main.rs:338:9 Aug 29 20:47:42.082 INFO kablam! | Aug 29 20:47:42.082 INFO kablam! 338 | let mut need_trim:bool; Aug 29 20:47:42.082 INFO kablam! | ----^^^^^^^^^ Aug 29 20:47:42.082 INFO kablam! | | Aug 29 20:47:42.082 INFO kablam! | help: remove this `mut` Aug 29 20:47:42.082 INFO kablam! Aug 29 20:47:42.082 INFO kablam! warning: variable does not need to be mutable Aug 29 20:47:42.082 INFO kablam! --> src/main.rs:355:9 Aug 29 20:47:42.082 INFO kablam! | Aug 29 20:47:42.082 INFO kablam! 355 | let mut chrom = 0; Aug 29 20:47:42.082 INFO kablam! | ----^^^^^ Aug 29 20:47:42.082 INFO kablam! | | Aug 29 20:47:42.082 INFO kablam! | help: remove this `mut` Aug 29 20:47:42.082 INFO kablam! Aug 29 20:47:42.084 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Aug 29 20:47:42.084 INFO kablam! --> src/main.rs:68:1 Aug 29 20:47:42.084 INFO kablam! | Aug 29 20:47:42.084 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Aug 29 20:47:42.084 INFO kablam! 69 | | Aug 29 20:47:42.084 INFO kablam! 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Aug 29 20:47:42.084 INFO kablam! 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Aug 29 20:47:42.084 INFO kablam! ... | Aug 29 20:47:42.084 INFO kablam! 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Aug 29 20:47:42.084 INFO kablam! 98 | | } Aug 29 20:47:42.084 INFO kablam! | |_^ Aug 29 20:47:42.084 INFO kablam! | Aug 29 20:47:42.084 INFO kablam! = note: #[warn(non_snake_case)] on by default Aug 29 20:47:42.084 INFO kablam! Aug 29 20:47:42.084 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Aug 29 20:47:42.085 INFO kablam! --> src/main.rs:147:9 Aug 29 20:47:42.085 INFO kablam! | Aug 29 20:47:42.085 INFO kablam! 147 | let mut baseEach_num_record = String::new(); Aug 29 20:47:42.085 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.085 INFO kablam! Aug 29 20:47:42.085 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Aug 29 20:47:42.085 INFO kablam! --> src/main.rs:148:9 Aug 29 20:47:42.085 INFO kablam! | Aug 29 20:47:42.085 INFO kablam! 148 | let mut baseEach_percent_record = String::new(); Aug 29 20:47:42.085 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.085 INFO kablam! Aug 29 20:47:42.085 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:42.085 INFO kablam! --> src/main.rs:267:9 Aug 29 20:47:42.085 INFO kablam! | Aug 29 20:47:42.085 INFO kablam! 267 | o_buff.write(&member_record.2); Aug 29 20:47:42.085 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.085 INFO kablam! | Aug 29 20:47:42.085 INFO kablam! = note: #[warn(unused_must_use)] on by default Aug 29 20:47:42.085 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:42.085 INFO kablam! Aug 29 20:47:42.085 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:42.085 INFO kablam! --> src/main.rs:269:9 Aug 29 20:47:42.085 INFO kablam! | Aug 29 20:47:42.085 INFO kablam! 269 | o_buff.write(&member_record.0); Aug 29 20:47:42.086 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.086 INFO kablam! | Aug 29 20:47:42.086 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:42.086 INFO kablam! Aug 29 20:47:42.086 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:42.086 INFO kablam! --> src/main.rs:272:9 Aug 29 20:47:42.086 INFO kablam! | Aug 29 20:47:42.086 INFO kablam! 272 | o_buff.write(&real_qual_temp); Aug 29 20:47:42.086 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.086 INFO kablam! | Aug 29 20:47:42.086 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:42.086 INFO kablam! Aug 29 20:47:42.086 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:42.086 INFO kablam! --> src/main.rs:274:5 Aug 29 20:47:42.086 INFO kablam! | Aug 29 20:47:42.086 INFO kablam! 274 | o_buff.write(b"\n"); Aug 29 20:47:42.086 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.086 INFO kablam! | Aug 29 20:47:42.086 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:42.086 INFO kablam! Aug 29 20:47:42.086 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:42.086 INFO kablam! --> src/main.rs:277:5 Aug 29 20:47:42.086 INFO kablam! | Aug 29 20:47:42.086 INFO kablam! 277 | o_buff.write(b"\n"); Aug 29 20:47:42.086 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.086 INFO kablam! | Aug 29 20:47:42.086 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:42.086 INFO kablam! Aug 29 20:47:42.087 INFO kablam! warning: unused `std::result::Result` which must be used Aug 29 20:47:42.087 INFO kablam! --> src/main.rs:280:5 Aug 29 20:47:42.087 INFO kablam! | Aug 29 20:47:42.087 INFO kablam! 280 | o_buff.write(b"\n"); Aug 29 20:47:42.087 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.087 INFO kablam! | Aug 29 20:47:42.087 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Aug 29 20:47:42.087 INFO kablam! Aug 29 20:47:42.087 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Aug 29 20:47:42.087 INFO kablam! --> src/main.rs:286:10 Aug 29 20:47:42.087 INFO kablam! | Aug 29 20:47:42.087 INFO kablam! 286 | for (key_dupGroup, pair_dup) in pd.iter() { Aug 29 20:47:42.087 INFO kablam! | ^^^^^^^^^^^^ Aug 29 20:47:42.087 INFO kablam! Aug 29 20:47:42.087 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Aug 29 20:47:42.087 INFO kablam! --> src/main.rs:357:9 Aug 29 20:47:42.087 INFO kablam! | Aug 29 20:47:42.087 INFO kablam! 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Aug 29 20:47:42.087 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^ Aug 29 20:47:42.087 INFO kablam! Aug 29 20:47:42.087 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Aug 29 20:47:42.087 INFO kablam! --> src/main.rs:387:17 Aug 29 20:47:42.087 INFO kablam! | Aug 29 20:47:42.087 INFO kablam! 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Aug 29 20:47:42.087 INFO kablam! | ^^^^^^^^^^^^ Aug 29 20:47:42.087 INFO kablam! Aug 29 20:47:42.115 INFO kablam! Finished dev [unoptimized + debuginfo] target(s) in 43.82s Aug 29 20:47:42.120 INFO kablam! su: No module specific data is present Aug 29 20:47:42.607 INFO running `"docker" "rm" "-f" "9c18a4432fa0345184d826a11bee3684bae6936231f9bf744b02602eb780689d"` Aug 29 20:47:42.771 INFO blam! 9c18a4432fa0345184d826a11bee3684bae6936231f9bf744b02602eb780689d