Sep 17 13:46:44.740 INFO checking TuBieJun/consensus against try#cfeeefe83c83bceb55d60d7e2be173db7597ed50 for pr-54033 Sep 17 13:46:44.740 INFO running: cargo +cfeeefe83c83bceb55d60d7e2be173db7597ed50-alt check --frozen --all --all-targets Sep 17 13:46:44.740 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-1/pr-54033/try#cfeeefe83c83bceb55d60d7e2be173db7597ed50:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-54033/worker-1/try#cfeeefe83c83bceb55d60d7e2be173db7597ed50:/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=1000" "-e" "CMD=cargo +cfeeefe83c83bceb55d60d7e2be173db7597ed50-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "1536M" "crater"` Sep 17 13:46:44.987 INFO blam! bf7c745bea00598752458c3f88c633b0e3970f33ea8fa251c3893ff5a548a95e Sep 17 13:46:44.989 INFO running `"docker" "start" "-a" "bf7c745bea00598752458c3f88c633b0e3970f33ea8fa251c3893ff5a548a95e"` Sep 17 13:46:45.627 INFO kablam! usermod: no changes Sep 17 13:46:45.717 INFO kablam! Compiling quick-error v1.2.1 Sep 17 13:46:45.722 INFO kablam! Checking custom_derive v0.1.7 Sep 17 13:46:45.722 INFO kablam! Checking ieee754 v0.2.2 Sep 17 13:46:45.725 INFO kablam! Checking itertools v0.6.5 Sep 17 13:46:45.725 INFO kablam! Checking atty v0.2.6 Sep 17 13:46:45.725 INFO kablam! Compiling newtype_derive v0.1.6 Sep 17 13:46:46.620 INFO kablam! Compiling fs-utils v1.0.0 Sep 17 13:46:46.743 INFO kablam! Checking clap v2.29.0 Sep 17 13:46:48.289 INFO kablam! Compiling rust-htslib v0.15.0 Sep 17 13:47:22.467 INFO kablam! Checking consensus v0.1.0 (/source) Sep 17 13:47:23.156 INFO kablam! warning: unused import: `std::env` Sep 17 13:47:23.156 INFO kablam! --> src/main.rs:12:5 Sep 17 13:47:23.156 INFO kablam! | Sep 17 13:47:23.156 INFO kablam! 12 | use std::env; Sep 17 13:47:23.156 INFO kablam! | ^^^^^^^^ Sep 17 13:47:23.156 INFO kablam! | Sep 17 13:47:23.156 INFO kablam! = note: #[warn(unused_imports)] on by default Sep 17 13:47:23.156 INFO kablam! Sep 17 13:47:23.157 INFO kablam! warning: unused import: `rust_htslib::prelude::*` Sep 17 13:47:23.157 INFO kablam! --> src/main.rs:16:5 Sep 17 13:47:23.157 INFO kablam! | Sep 17 13:47:23.157 INFO kablam! 16 | use rust_htslib::prelude::*; Sep 17 13:47:23.157 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.157 INFO kablam! Sep 17 13:47:23.157 INFO kablam! warning: unused import: `std::io` Sep 17 13:47:23.157 INFO kablam! --> src/main.rs:21:5 Sep 17 13:47:23.157 INFO kablam! | Sep 17 13:47:23.157 INFO kablam! 21 | use std::io; Sep 17 13:47:23.157 INFO kablam! | ^^^^^^^ Sep 17 13:47:23.157 INFO kablam! Sep 17 13:47:23.157 INFO kablam! warning: unused import: `PathBuf` Sep 17 13:47:23.157 INFO kablam! --> src/main.rs:25:23 Sep 17 13:47:23.157 INFO kablam! | Sep 17 13:47:23.157 INFO kablam! 25 | use std::path::{Path, PathBuf}; Sep 17 13:47:23.157 INFO kablam! | ^^^^^^^ Sep 17 13:47:23.157 INFO kablam! Sep 17 13:47:23.157 INFO kablam! warning: unused import: `SubCommand` Sep 17 13:47:23.157 INFO kablam! --> src/main.rs:26:22 Sep 17 13:47:23.157 INFO kablam! | Sep 17 13:47:23.157 INFO kablam! 26 | use clap::{Arg, App, SubCommand}; Sep 17 13:47:23.157 INFO kablam! | ^^^^^^^^^^ Sep 17 13:47:23.157 INFO kablam! Sep 17 13:47:23.163 INFO kablam! warning: unnecessary parentheses around `if` condition Sep 17 13:47:23.163 INFO kablam! --> src/main.rs:218:20 Sep 17 13:47:23.163 INFO kablam! | Sep 17 13:47:23.163 INFO kablam! 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Sep 17 13:47:23.163 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Sep 17 13:47:23.163 INFO kablam! | Sep 17 13:47:23.163 INFO kablam! = note: #[warn(unused_parens)] on by default Sep 17 13:47:23.163 INFO kablam! Sep 17 13:47:23.163 INFO kablam! warning: unnecessary parentheses around `if` condition Sep 17 13:47:23.163 INFO kablam! --> src/main.rs:239:16 Sep 17 13:47:23.163 INFO kablam! | Sep 17 13:47:23.163 INFO kablam! 239 | if (baseEach_percent_record.len() > 0) { Sep 17 13:47:23.163 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Sep 17 13:47:23.163 INFO kablam! Sep 17 13:47:23.267 INFO kablam! warning: unused import: `std::env` Sep 17 13:47:23.267 INFO kablam! --> src/main.rs:12:5 Sep 17 13:47:23.267 INFO kablam! | Sep 17 13:47:23.267 INFO kablam! 12 | use std::env; Sep 17 13:47:23.267 INFO kablam! | ^^^^^^^^ Sep 17 13:47:23.267 INFO kablam! | Sep 17 13:47:23.267 INFO kablam! = note: #[warn(unused_imports)] on by default Sep 17 13:47:23.267 INFO kablam! Sep 17 13:47:23.267 INFO kablam! warning: unused import: `rust_htslib::prelude::*` Sep 17 13:47:23.267 INFO kablam! --> src/main.rs:16:5 Sep 17 13:47:23.267 INFO kablam! | Sep 17 13:47:23.267 INFO kablam! 16 | use rust_htslib::prelude::*; Sep 17 13:47:23.267 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.267 INFO kablam! Sep 17 13:47:23.267 INFO kablam! warning: unused import: `std::io` Sep 17 13:47:23.267 INFO kablam! --> src/main.rs:21:5 Sep 17 13:47:23.267 INFO kablam! | Sep 17 13:47:23.267 INFO kablam! 21 | use std::io; Sep 17 13:47:23.267 INFO kablam! | ^^^^^^^ Sep 17 13:47:23.267 INFO kablam! Sep 17 13:47:23.267 INFO kablam! warning: unused import: `PathBuf` Sep 17 13:47:23.267 INFO kablam! --> src/main.rs:25:23 Sep 17 13:47:23.267 INFO kablam! | Sep 17 13:47:23.267 INFO kablam! 25 | use std::path::{Path, PathBuf}; Sep 17 13:47:23.267 INFO kablam! | ^^^^^^^ Sep 17 13:47:23.267 INFO kablam! Sep 17 13:47:23.267 INFO kablam! warning: unused import: `SubCommand` Sep 17 13:47:23.267 INFO kablam! --> src/main.rs:26:22 Sep 17 13:47:23.267 INFO kablam! | Sep 17 13:47:23.267 INFO kablam! 26 | use clap::{Arg, App, SubCommand}; Sep 17 13:47:23.267 INFO kablam! | ^^^^^^^^^^ Sep 17 13:47:23.267 INFO kablam! Sep 17 13:47:23.267 INFO kablam! warning: unnecessary parentheses around `if` condition Sep 17 13:47:23.267 INFO kablam! --> src/main.rs:218:20 Sep 17 13:47:23.267 INFO kablam! | Sep 17 13:47:23.267 INFO kablam! 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Sep 17 13:47:23.267 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Sep 17 13:47:23.267 INFO kablam! | Sep 17 13:47:23.267 INFO kablam! = note: #[warn(unused_parens)] on by default Sep 17 13:47:23.267 INFO kablam! Sep 17 13:47:23.267 INFO kablam! warning: unnecessary parentheses around `if` condition Sep 17 13:47:23.267 INFO kablam! --> src/main.rs:239:16 Sep 17 13:47:23.267 INFO kablam! | Sep 17 13:47:23.267 INFO kablam! 239 | if (baseEach_percent_record.len() > 0) { Sep 17 13:47:23.267 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Sep 17 13:47:23.268 INFO kablam! Sep 17 13:47:23.339 INFO kablam! warning: unused import: `std::io::prelude` Sep 17 13:47:23.339 INFO kablam! --> src/main.rs:22:5 Sep 17 13:47:23.339 INFO kablam! | Sep 17 13:47:23.339 INFO kablam! 22 | use std::io::prelude::*; Sep 17 13:47:23.339 INFO kablam! | ^^^^^^^^^^^^^^^^ Sep 17 13:47:23.339 INFO kablam! Sep 17 13:47:23.387 INFO kablam! warning: unused variable: `consensus_base` Sep 17 13:47:23.387 INFO kablam! --> src/main.rs:139:9 Sep 17 13:47:23.387 INFO kablam! | Sep 17 13:47:23.387 INFO kablam! 139 | let consensus_base:Vec = Vec::new(); Sep 17 13:47:23.387 INFO kablam! | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Sep 17 13:47:23.387 INFO kablam! | Sep 17 13:47:23.387 INFO kablam! = note: #[warn(unused_variables)] on by default Sep 17 13:47:23.387 INFO kablam! Sep 17 13:47:23.387 INFO kablam! warning: unused variable: `consensus_source_reads` Sep 17 13:47:23.387 INFO kablam! --> src/main.rs:144:13 Sep 17 13:47:23.387 INFO kablam! | Sep 17 13:47:23.387 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Sep 17 13:47:23.387 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Sep 17 13:47:23.387 INFO kablam! Sep 17 13:47:23.387 INFO kablam! warning: unused variable: `chrom` Sep 17 13:47:23.387 INFO kablam! --> src/main.rs:283:121 Sep 17 13:47:23.387 INFO kablam! | Sep 17 13:47:23.387 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) { Sep 17 13:47:23.387 INFO kablam! | ^^^^^ help: consider using `_chrom` instead Sep 17 13:47:23.387 INFO kablam! Sep 17 13:47:23.387 INFO kablam! warning: value assigned to `new_seq_b` is never read Sep 17 13:47:23.387 INFO kablam! --> src/main.rs:370:21 Sep 17 13:47:23.387 INFO kablam! | Sep 17 13:47:23.387 INFO kablam! 370 | let mut new_seq_b:Vec = Vec::new(); Sep 17 13:47:23.387 INFO kablam! | ^^^^^^^^^ Sep 17 13:47:23.387 INFO kablam! | Sep 17 13:47:23.387 INFO kablam! = note: #[warn(unused_assignments)] on by default Sep 17 13:47:23.387 INFO kablam! Sep 17 13:47:23.407 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.407 INFO kablam! --> src/main.rs:74:9 Sep 17 13:47:23.407 INFO kablam! | Sep 17 13:47:23.407 INFO kablam! 74 | let mut pair; Sep 17 13:47:23.407 INFO kablam! | ----^^^^ Sep 17 13:47:23.407 INFO kablam! | | Sep 17 13:47:23.407 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.407 INFO kablam! | Sep 17 13:47:23.407 INFO kablam! = note: #[warn(unused_mut)] on by default Sep 17 13:47:23.407 INFO kablam! Sep 17 13:47:23.407 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.407 INFO kablam! --> src/main.rs:75:9 Sep 17 13:47:23.407 INFO kablam! | Sep 17 13:47:23.407 INFO kablam! 75 | let mut strand; Sep 17 13:47:23.407 INFO kablam! | ----^^^^^^ Sep 17 13:47:23.407 INFO kablam! | | Sep 17 13:47:23.407 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.407 INFO kablam! Sep 17 13:47:23.407 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.407 INFO kablam! --> src/main.rs:76:9 Sep 17 13:47:23.407 INFO kablam! | Sep 17 13:47:23.407 INFO kablam! 76 | let mut aln_pos; Sep 17 13:47:23.407 INFO kablam! | ----^^^^^^^ Sep 17 13:47:23.407 INFO kablam! | | Sep 17 13:47:23.407 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.407 INFO kablam! Sep 17 13:47:23.455 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.455 INFO kablam! --> src/main.rs:144:9 Sep 17 13:47:23.455 INFO kablam! | Sep 17 13:47:23.455 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Sep 17 13:47:23.455 INFO kablam! | ----^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.455 INFO kablam! | | Sep 17 13:47:23.455 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.455 INFO kablam! Sep 17 13:47:23.455 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.455 INFO kablam! --> src/main.rs:151:9 Sep 17 13:47:23.455 INFO kablam! | Sep 17 13:47:23.455 INFO kablam! 151 | let mut top_cigar:&CigarStringView; Sep 17 13:47:23.455 INFO kablam! | ----^^^^^^^^^ Sep 17 13:47:23.455 INFO kablam! | | Sep 17 13:47:23.455 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.455 INFO kablam! Sep 17 13:47:23.487 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.487 INFO kablam! --> src/main.rs:338:9 Sep 17 13:47:23.487 INFO kablam! | Sep 17 13:47:23.487 INFO kablam! 338 | let mut need_trim:bool; Sep 17 13:47:23.487 INFO kablam! | ----^^^^^^^^^ Sep 17 13:47:23.487 INFO kablam! | | Sep 17 13:47:23.487 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.487 INFO kablam! Sep 17 13:47:23.487 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.487 INFO kablam! --> src/main.rs:355:9 Sep 17 13:47:23.487 INFO kablam! | Sep 17 13:47:23.487 INFO kablam! 355 | let mut chrom = 0; Sep 17 13:47:23.487 INFO kablam! | ----^^^^^ Sep 17 13:47:23.487 INFO kablam! | | Sep 17 13:47:23.487 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.487 INFO kablam! Sep 17 13:47:23.487 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Sep 17 13:47:23.487 INFO kablam! --> src/main.rs:68:1 Sep 17 13:47:23.487 INFO kablam! | Sep 17 13:47:23.487 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Sep 17 13:47:23.487 INFO kablam! 69 | | Sep 17 13:47:23.487 INFO kablam! 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Sep 17 13:47:23.487 INFO kablam! 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Sep 17 13:47:23.487 INFO kablam! ... | Sep 17 13:47:23.487 INFO kablam! 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Sep 17 13:47:23.487 INFO kablam! 98 | | } Sep 17 13:47:23.487 INFO kablam! | |_^ Sep 17 13:47:23.487 INFO kablam! | Sep 17 13:47:23.487 INFO kablam! = note: #[warn(non_snake_case)] on by default Sep 17 13:47:23.487 INFO kablam! Sep 17 13:47:23.487 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Sep 17 13:47:23.487 INFO kablam! --> src/main.rs:147:9 Sep 17 13:47:23.487 INFO kablam! | Sep 17 13:47:23.487 INFO kablam! 147 | let mut baseEach_num_record = String::new(); Sep 17 13:47:23.487 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.487 INFO kablam! Sep 17 13:47:23.487 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Sep 17 13:47:23.487 INFO kablam! --> src/main.rs:148:9 Sep 17 13:47:23.488 INFO kablam! | Sep 17 13:47:23.488 INFO kablam! 148 | let mut baseEach_percent_record = String::new(); Sep 17 13:47:23.488 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.488 INFO kablam! Sep 17 13:47:23.499 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.499 INFO kablam! --> src/main.rs:267:9 Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! 267 | o_buff.write(&member_record.2); Sep 17 13:47:23.499 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! = note: #[warn(unused_must_use)] on by default Sep 17 13:47:23.499 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.499 INFO kablam! Sep 17 13:47:23.499 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.499 INFO kablam! --> src/main.rs:269:9 Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! 269 | o_buff.write(&member_record.0); Sep 17 13:47:23.499 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.499 INFO kablam! Sep 17 13:47:23.499 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.499 INFO kablam! --> src/main.rs:272:9 Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! 272 | o_buff.write(&real_qual_temp); Sep 17 13:47:23.499 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.499 INFO kablam! Sep 17 13:47:23.499 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.499 INFO kablam! --> src/main.rs:274:5 Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! 274 | o_buff.write(b"\n"); Sep 17 13:47:23.499 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.499 INFO kablam! Sep 17 13:47:23.499 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.499 INFO kablam! --> src/main.rs:277:5 Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! 277 | o_buff.write(b"\n"); Sep 17 13:47:23.499 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.499 INFO kablam! Sep 17 13:47:23.499 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.499 INFO kablam! --> src/main.rs:280:5 Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! 280 | o_buff.write(b"\n"); Sep 17 13:47:23.499 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.499 INFO kablam! Sep 17 13:47:23.499 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Sep 17 13:47:23.499 INFO kablam! --> src/main.rs:286:10 Sep 17 13:47:23.499 INFO kablam! | Sep 17 13:47:23.499 INFO kablam! 286 | for (key_dupGroup, pair_dup) in pd.iter() { Sep 17 13:47:23.500 INFO kablam! | ^^^^^^^^^^^^ Sep 17 13:47:23.500 INFO kablam! Sep 17 13:47:23.500 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Sep 17 13:47:23.500 INFO kablam! --> src/main.rs:357:9 Sep 17 13:47:23.500 INFO kablam! | Sep 17 13:47:23.500 INFO kablam! 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Sep 17 13:47:23.500 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.500 INFO kablam! Sep 17 13:47:23.500 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Sep 17 13:47:23.500 INFO kablam! --> src/main.rs:387:17 Sep 17 13:47:23.500 INFO kablam! | Sep 17 13:47:23.500 INFO kablam! 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Sep 17 13:47:23.500 INFO kablam! | ^^^^^^^^^^^^ Sep 17 13:47:23.500 INFO kablam! Sep 17 13:47:23.615 INFO kablam! warning: unused import: `std::io::prelude` Sep 17 13:47:23.615 INFO kablam! --> src/main.rs:22:5 Sep 17 13:47:23.615 INFO kablam! | Sep 17 13:47:23.615 INFO kablam! 22 | use std::io::prelude::*; Sep 17 13:47:23.615 INFO kablam! | ^^^^^^^^^^^^^^^^ Sep 17 13:47:23.615 INFO kablam! Sep 17 13:47:23.646 INFO kablam! warning: unused variable: `consensus_base` Sep 17 13:47:23.646 INFO kablam! --> src/main.rs:139:9 Sep 17 13:47:23.646 INFO kablam! | Sep 17 13:47:23.646 INFO kablam! 139 | let consensus_base:Vec = Vec::new(); Sep 17 13:47:23.646 INFO kablam! | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Sep 17 13:47:23.646 INFO kablam! | Sep 17 13:47:23.646 INFO kablam! = note: #[warn(unused_variables)] on by default Sep 17 13:47:23.646 INFO kablam! Sep 17 13:47:23.646 INFO kablam! warning: unused variable: `consensus_source_reads` Sep 17 13:47:23.646 INFO kablam! --> src/main.rs:144:13 Sep 17 13:47:23.646 INFO kablam! | Sep 17 13:47:23.646 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Sep 17 13:47:23.646 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Sep 17 13:47:23.646 INFO kablam! Sep 17 13:47:23.646 INFO kablam! warning: unused variable: `chrom` Sep 17 13:47:23.646 INFO kablam! --> src/main.rs:283:121 Sep 17 13:47:23.646 INFO kablam! | Sep 17 13:47:23.646 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) { Sep 17 13:47:23.646 INFO kablam! | ^^^^^ help: consider using `_chrom` instead Sep 17 13:47:23.646 INFO kablam! Sep 17 13:47:23.651 INFO kablam! warning: value assigned to `new_seq_b` is never read Sep 17 13:47:23.651 INFO kablam! --> src/main.rs:370:21 Sep 17 13:47:23.651 INFO kablam! | Sep 17 13:47:23.651 INFO kablam! 370 | let mut new_seq_b:Vec = Vec::new(); Sep 17 13:47:23.651 INFO kablam! | ^^^^^^^^^ Sep 17 13:47:23.651 INFO kablam! | Sep 17 13:47:23.651 INFO kablam! = note: #[warn(unused_assignments)] on by default Sep 17 13:47:23.651 INFO kablam! Sep 17 13:47:23.655 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.655 INFO kablam! --> src/main.rs:74:9 Sep 17 13:47:23.655 INFO kablam! | Sep 17 13:47:23.655 INFO kablam! 74 | let mut pair; Sep 17 13:47:23.655 INFO kablam! | ----^^^^ Sep 17 13:47:23.655 INFO kablam! | | Sep 17 13:47:23.655 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.655 INFO kablam! | Sep 17 13:47:23.655 INFO kablam! = note: #[warn(unused_mut)] on by default Sep 17 13:47:23.655 INFO kablam! Sep 17 13:47:23.655 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.655 INFO kablam! --> src/main.rs:75:9 Sep 17 13:47:23.655 INFO kablam! | Sep 17 13:47:23.655 INFO kablam! 75 | let mut strand; Sep 17 13:47:23.655 INFO kablam! | ----^^^^^^ Sep 17 13:47:23.655 INFO kablam! | | Sep 17 13:47:23.655 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.655 INFO kablam! Sep 17 13:47:23.655 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.655 INFO kablam! --> src/main.rs:76:9 Sep 17 13:47:23.655 INFO kablam! | Sep 17 13:47:23.655 INFO kablam! 76 | let mut aln_pos; Sep 17 13:47:23.655 INFO kablam! | ----^^^^^^^ Sep 17 13:47:23.655 INFO kablam! | | Sep 17 13:47:23.655 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.655 INFO kablam! Sep 17 13:47:23.683 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.683 INFO kablam! --> src/main.rs:144:9 Sep 17 13:47:23.683 INFO kablam! | Sep 17 13:47:23.683 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Sep 17 13:47:23.683 INFO kablam! | ----^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.683 INFO kablam! | | Sep 17 13:47:23.683 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.683 INFO kablam! Sep 17 13:47:23.683 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.683 INFO kablam! --> src/main.rs:151:9 Sep 17 13:47:23.683 INFO kablam! | Sep 17 13:47:23.683 INFO kablam! 151 | let mut top_cigar:&CigarStringView; Sep 17 13:47:23.683 INFO kablam! | ----^^^^^^^^^ Sep 17 13:47:23.683 INFO kablam! | | Sep 17 13:47:23.683 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.683 INFO kablam! Sep 17 13:47:23.703 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.703 INFO kablam! --> src/main.rs:338:9 Sep 17 13:47:23.703 INFO kablam! | Sep 17 13:47:23.703 INFO kablam! 338 | let mut need_trim:bool; Sep 17 13:47:23.703 INFO kablam! | ----^^^^^^^^^ Sep 17 13:47:23.703 INFO kablam! | | Sep 17 13:47:23.703 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.703 INFO kablam! Sep 17 13:47:23.703 INFO kablam! warning: variable does not need to be mutable Sep 17 13:47:23.703 INFO kablam! --> src/main.rs:355:9 Sep 17 13:47:23.703 INFO kablam! | Sep 17 13:47:23.703 INFO kablam! 355 | let mut chrom = 0; Sep 17 13:47:23.703 INFO kablam! | ----^^^^^ Sep 17 13:47:23.703 INFO kablam! | | Sep 17 13:47:23.703 INFO kablam! | help: remove this `mut` Sep 17 13:47:23.703 INFO kablam! Sep 17 13:47:23.703 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Sep 17 13:47:23.703 INFO kablam! --> src/main.rs:68:1 Sep 17 13:47:23.703 INFO kablam! | Sep 17 13:47:23.703 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Sep 17 13:47:23.703 INFO kablam! 69 | | Sep 17 13:47:23.703 INFO kablam! 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Sep 17 13:47:23.703 INFO kablam! 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Sep 17 13:47:23.703 INFO kablam! ... | Sep 17 13:47:23.704 INFO kablam! 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Sep 17 13:47:23.704 INFO kablam! 98 | | } Sep 17 13:47:23.704 INFO kablam! | |_^ Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! = note: #[warn(non_snake_case)] on by default Sep 17 13:47:23.704 INFO kablam! Sep 17 13:47:23.704 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Sep 17 13:47:23.704 INFO kablam! --> src/main.rs:147:9 Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! 147 | let mut baseEach_num_record = String::new(); Sep 17 13:47:23.704 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.704 INFO kablam! Sep 17 13:47:23.704 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Sep 17 13:47:23.704 INFO kablam! --> src/main.rs:148:9 Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! 148 | let mut baseEach_percent_record = String::new(); Sep 17 13:47:23.704 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.704 INFO kablam! Sep 17 13:47:23.704 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.704 INFO kablam! --> src/main.rs:267:9 Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! 267 | o_buff.write(&member_record.2); Sep 17 13:47:23.704 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! = note: #[warn(unused_must_use)] on by default Sep 17 13:47:23.704 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.704 INFO kablam! Sep 17 13:47:23.704 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.704 INFO kablam! --> src/main.rs:269:9 Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! 269 | o_buff.write(&member_record.0); Sep 17 13:47:23.704 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.704 INFO kablam! Sep 17 13:47:23.704 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.704 INFO kablam! --> src/main.rs:272:9 Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! 272 | o_buff.write(&real_qual_temp); Sep 17 13:47:23.704 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.704 INFO kablam! Sep 17 13:47:23.704 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.704 INFO kablam! --> src/main.rs:274:5 Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! 274 | o_buff.write(b"\n"); Sep 17 13:47:23.704 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.704 INFO kablam! Sep 17 13:47:23.704 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.704 INFO kablam! --> src/main.rs:277:5 Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! 277 | o_buff.write(b"\n"); Sep 17 13:47:23.704 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.704 INFO kablam! | Sep 17 13:47:23.704 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.704 INFO kablam! Sep 17 13:47:23.705 INFO kablam! warning: unused `std::result::Result` which must be used Sep 17 13:47:23.705 INFO kablam! --> src/main.rs:280:5 Sep 17 13:47:23.705 INFO kablam! | Sep 17 13:47:23.705 INFO kablam! 280 | o_buff.write(b"\n"); Sep 17 13:47:23.705 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.705 INFO kablam! | Sep 17 13:47:23.705 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 17 13:47:23.705 INFO kablam! Sep 17 13:47:23.705 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Sep 17 13:47:23.705 INFO kablam! --> src/main.rs:286:10 Sep 17 13:47:23.705 INFO kablam! | Sep 17 13:47:23.705 INFO kablam! 286 | for (key_dupGroup, pair_dup) in pd.iter() { Sep 17 13:47:23.705 INFO kablam! | ^^^^^^^^^^^^ Sep 17 13:47:23.705 INFO kablam! Sep 17 13:47:23.705 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Sep 17 13:47:23.705 INFO kablam! --> src/main.rs:357:9 Sep 17 13:47:23.705 INFO kablam! | Sep 17 13:47:23.705 INFO kablam! 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Sep 17 13:47:23.705 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^ Sep 17 13:47:23.705 INFO kablam! Sep 17 13:47:23.705 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Sep 17 13:47:23.705 INFO kablam! --> src/main.rs:387:17 Sep 17 13:47:23.705 INFO kablam! | Sep 17 13:47:23.705 INFO kablam! 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Sep 17 13:47:23.705 INFO kablam! | ^^^^^^^^^^^^ Sep 17 13:47:23.705 INFO kablam! Sep 17 13:47:23.743 INFO kablam! Finished dev [unoptimized + debuginfo] target(s) in 38.08s Sep 17 13:47:23.751 INFO kablam! su: No module specific data is present Sep 17 13:47:25.181 INFO running `"docker" "rm" "-f" "bf7c745bea00598752458c3f88c633b0e3970f33ea8fa251c3893ff5a548a95e"` Sep 17 13:47:25.584 INFO blam! bf7c745bea00598752458c3f88c633b0e3970f33ea8fa251c3893ff5a548a95e