Nov 01 09:41:40.594 INFO checking TuBieJun/consensus against try#d7816399d50d407bbce1efe9dbadf8faaaf568fc for pr-55538 Nov 01 09:41:40.594 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-55538/worker-7/try#d7816399d50d407bbce1efe9dbadf8faaaf568fc:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-7/pr-55538/try#d7816399d50d407bbce1efe9dbadf8faaaf568fc:/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 +d7816399d50d407bbce1efe9dbadf8faaaf568fc-alt check --frozen --all --all-targets" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"` Nov 01 09:41:41.060 INFO blam! 572c445341b250c9fef4633898f45a280117c08f2875c3eef613da8fb8a7fb85 Nov 01 09:41:41.066 INFO running `"docker" "start" "-a" "572c445341b250c9fef4633898f45a280117c08f2875c3eef613da8fb8a7fb85"` Nov 01 09:41:42.593 INFO kablam! usermod: no changes Nov 01 09:41:42.812 INFO kablam! Compiling fs-utils v1.0.0 Nov 01 09:41:43.995 INFO kablam! Compiling rust-htslib v0.15.0 Nov 01 09:42:12.861 INFO kablam! Checking consensus v0.1.0 (/source) Nov 01 09:42:15.188 INFO kablam! warning: unused import: `std::env` Nov 01 09:42:15.189 INFO kablam! --> src/main.rs:12:5 Nov 01 09:42:15.190 INFO kablam! | Nov 01 09:42:15.191 INFO kablam! 12 | use std::env; Nov 01 09:42:15.191 INFO kablam! | ^^^^^^^^ Nov 01 09:42:15.192 INFO kablam! | Nov 01 09:42:15.192 INFO kablam! = note: #[warn(unused_imports)] on by default Nov 01 09:42:15.193 INFO kablam! Nov 01 09:42:15.193 INFO kablam! warning: unused import: `rust_htslib::prelude::*` Nov 01 09:42:15.194 INFO kablam! --> src/main.rs:16:5 Nov 01 09:42:15.194 INFO kablam! | Nov 01 09:42:15.195 INFO kablam! 16 | use rust_htslib::prelude::*; Nov 01 09:42:15.195 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.196 INFO kablam! Nov 01 09:42:15.196 INFO kablam! warning: unused import: `std::io` Nov 01 09:42:15.197 INFO kablam! --> src/main.rs:21:5 Nov 01 09:42:15.197 INFO kablam! | Nov 01 09:42:15.198 INFO kablam! 21 | use std::io; Nov 01 09:42:15.198 INFO kablam! | ^^^^^^^ Nov 01 09:42:15.199 INFO kablam! Nov 01 09:42:15.199 INFO kablam! warning: unused import: `PathBuf` Nov 01 09:42:15.200 INFO kablam! --> src/main.rs:25:23 Nov 01 09:42:15.200 INFO kablam! | Nov 01 09:42:15.201 INFO kablam! 25 | use std::path::{Path, PathBuf}; Nov 01 09:42:15.201 INFO kablam! | ^^^^^^^ Nov 01 09:42:15.202 INFO kablam! Nov 01 09:42:15.202 INFO kablam! warning: unused import: `SubCommand` Nov 01 09:42:15.203 INFO kablam! --> src/main.rs:26:22 Nov 01 09:42:15.203 INFO kablam! | Nov 01 09:42:15.204 INFO kablam! 26 | use clap::{Arg, App, SubCommand}; Nov 01 09:42:15.204 INFO kablam! | ^^^^^^^^^^ Nov 01 09:42:15.205 INFO kablam! Nov 01 09:42:15.205 INFO kablam! warning: unnecessary parentheses around `if` condition Nov 01 09:42:15.205 INFO kablam! --> src/main.rs:218:20 Nov 01 09:42:15.206 INFO kablam! | Nov 01 09:42:15.206 INFO kablam! 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Nov 01 09:42:15.206 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Nov 01 09:42:15.206 INFO kablam! | Nov 01 09:42:15.206 INFO kablam! = note: #[warn(unused_parens)] on by default Nov 01 09:42:15.206 INFO kablam! Nov 01 09:42:15.212 INFO kablam! warning: unnecessary parentheses around `if` condition Nov 01 09:42:15.212 INFO kablam! --> src/main.rs:239:16 Nov 01 09:42:15.212 INFO kablam! | Nov 01 09:42:15.212 INFO kablam! 239 | if (baseEach_percent_record.len() > 0) { Nov 01 09:42:15.212 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Nov 01 09:42:15.213 INFO kablam! Nov 01 09:42:15.410 INFO kablam! warning: unused import: `std::env` Nov 01 09:42:15.410 INFO kablam! --> src/main.rs:12:5 Nov 01 09:42:15.410 INFO kablam! | Nov 01 09:42:15.410 INFO kablam! 12 | use std::env; Nov 01 09:42:15.410 INFO kablam! | ^^^^^^^^ Nov 01 09:42:15.410 INFO kablam! | Nov 01 09:42:15.410 INFO kablam! = note: #[warn(unused_imports)] on by default Nov 01 09:42:15.410 INFO kablam! Nov 01 09:42:15.410 INFO kablam! warning: unused import: `rust_htslib::prelude::*` Nov 01 09:42:15.410 INFO kablam! --> src/main.rs:16:5 Nov 01 09:42:15.410 INFO kablam! | Nov 01 09:42:15.410 INFO kablam! 16 | use rust_htslib::prelude::*; Nov 01 09:42:15.410 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.411 INFO kablam! Nov 01 09:42:15.411 INFO kablam! warning: unused import: `std::io` Nov 01 09:42:15.411 INFO kablam! --> src/main.rs:21:5 Nov 01 09:42:15.411 INFO kablam! | Nov 01 09:42:15.411 INFO kablam! 21 | use std::io; Nov 01 09:42:15.411 INFO kablam! | ^^^^^^^ Nov 01 09:42:15.411 INFO kablam! Nov 01 09:42:15.411 INFO kablam! warning: unused import: `PathBuf` Nov 01 09:42:15.411 INFO kablam! --> src/main.rs:25:23 Nov 01 09:42:15.411 INFO kablam! | Nov 01 09:42:15.411 INFO kablam! 25 | use std::path::{Path, PathBuf}; Nov 01 09:42:15.412 INFO kablam! | ^^^^^^^ Nov 01 09:42:15.412 INFO kablam! Nov 01 09:42:15.412 INFO kablam! warning: unused import: `SubCommand` Nov 01 09:42:15.412 INFO kablam! --> src/main.rs:26:22 Nov 01 09:42:15.412 INFO kablam! | Nov 01 09:42:15.412 INFO kablam! 26 | use clap::{Arg, App, SubCommand}; Nov 01 09:42:15.412 INFO kablam! | ^^^^^^^^^^ Nov 01 09:42:15.412 INFO kablam! Nov 01 09:42:15.412 INFO kablam! warning: unnecessary parentheses around `if` condition Nov 01 09:42:15.412 INFO kablam! --> src/main.rs:218:20 Nov 01 09:42:15.412 INFO kablam! | Nov 01 09:42:15.412 INFO kablam! 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Nov 01 09:42:15.414 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Nov 01 09:42:15.415 INFO kablam! | Nov 01 09:42:15.415 INFO kablam! = note: #[warn(unused_parens)] on by default Nov 01 09:42:15.415 INFO kablam! Nov 01 09:42:15.415 INFO kablam! warning: unnecessary parentheses around `if` condition Nov 01 09:42:15.415 INFO kablam! --> src/main.rs:239:16 Nov 01 09:42:15.415 INFO kablam! | Nov 01 09:42:15.416 INFO kablam! 239 | if (baseEach_percent_record.len() > 0) { Nov 01 09:42:15.416 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Nov 01 09:42:15.416 INFO kablam! Nov 01 09:42:15.435 INFO kablam! warning: unused import: `std::io::prelude` Nov 01 09:42:15.435 INFO kablam! --> src/main.rs:22:5 Nov 01 09:42:15.435 INFO kablam! | Nov 01 09:42:15.435 INFO kablam! 22 | use std::io::prelude::*; Nov 01 09:42:15.435 INFO kablam! | ^^^^^^^^^^^^^^^^ Nov 01 09:42:15.435 INFO kablam! Nov 01 09:42:15.448 INFO kablam! warning: unused variable: `consensus_base` Nov 01 09:42:15.448 INFO kablam! --> src/main.rs:139:9 Nov 01 09:42:15.448 INFO kablam! | Nov 01 09:42:15.448 INFO kablam! 139 | let consensus_base:Vec = Vec::new(); Nov 01 09:42:15.448 INFO kablam! | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Nov 01 09:42:15.449 INFO kablam! | Nov 01 09:42:15.449 INFO kablam! = note: #[warn(unused_variables)] on by default Nov 01 09:42:15.449 INFO kablam! Nov 01 09:42:15.450 INFO kablam! warning: unused variable: `consensus_source_reads` Nov 01 09:42:15.450 INFO kablam! --> src/main.rs:144:13 Nov 01 09:42:15.450 INFO kablam! | Nov 01 09:42:15.450 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Nov 01 09:42:15.450 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Nov 01 09:42:15.450 INFO kablam! Nov 01 09:42:15.451 INFO kablam! warning: unused variable: `chrom` Nov 01 09:42:15.451 INFO kablam! --> src/main.rs:283:121 Nov 01 09:42:15.451 INFO kablam! | Nov 01 09:42:15.451 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) { Nov 01 09:42:15.451 INFO kablam! | ^^^^^ help: consider using `_chrom` instead Nov 01 09:42:15.452 INFO kablam! Nov 01 09:42:15.452 INFO kablam! warning: value assigned to `new_seq_b` is never read Nov 01 09:42:15.453 INFO kablam! --> src/main.rs:370:21 Nov 01 09:42:15.453 INFO kablam! | Nov 01 09:42:15.453 INFO kablam! 370 | let mut new_seq_b:Vec = Vec::new(); Nov 01 09:42:15.453 INFO kablam! | ^^^^^^^^^ Nov 01 09:42:15.453 INFO kablam! | Nov 01 09:42:15.454 INFO kablam! = note: #[warn(unused_assignments)] on by default Nov 01 09:42:15.454 INFO kablam! Nov 01 09:42:15.463 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.464 INFO kablam! --> src/main.rs:74:9 Nov 01 09:42:15.464 INFO kablam! | Nov 01 09:42:15.464 INFO kablam! 74 | let mut pair; Nov 01 09:42:15.464 INFO kablam! | ----^^^^ Nov 01 09:42:15.464 INFO kablam! | | Nov 01 09:42:15.464 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.465 INFO kablam! | Nov 01 09:42:15.465 INFO kablam! = note: #[warn(unused_mut)] on by default Nov 01 09:42:15.465 INFO kablam! Nov 01 09:42:15.465 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.465 INFO kablam! --> src/main.rs:75:9 Nov 01 09:42:15.466 INFO kablam! | Nov 01 09:42:15.466 INFO kablam! 75 | let mut strand; Nov 01 09:42:15.466 INFO kablam! | ----^^^^^^ Nov 01 09:42:15.466 INFO kablam! | | Nov 01 09:42:15.466 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.466 INFO kablam! Nov 01 09:42:15.467 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.467 INFO kablam! --> src/main.rs:76:9 Nov 01 09:42:15.467 INFO kablam! | Nov 01 09:42:15.468 INFO kablam! 76 | let mut aln_pos; Nov 01 09:42:15.468 INFO kablam! | ----^^^^^^^ Nov 01 09:42:15.468 INFO kablam! | | Nov 01 09:42:15.468 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.468 INFO kablam! Nov 01 09:42:15.536 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.536 INFO kablam! --> src/main.rs:144:9 Nov 01 09:42:15.537 INFO kablam! | Nov 01 09:42:15.537 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Nov 01 09:42:15.537 INFO kablam! | ----^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.537 INFO kablam! | | Nov 01 09:42:15.538 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.538 INFO kablam! Nov 01 09:42:15.539 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.539 INFO kablam! --> src/main.rs:151:9 Nov 01 09:42:15.539 INFO kablam! | Nov 01 09:42:15.539 INFO kablam! 151 | let mut top_cigar:&CigarStringView; Nov 01 09:42:15.539 INFO kablam! | ----^^^^^^^^^ Nov 01 09:42:15.539 INFO kablam! | | Nov 01 09:42:15.539 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.539 INFO kablam! Nov 01 09:42:15.568 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.568 INFO kablam! --> src/main.rs:338:9 Nov 01 09:42:15.568 INFO kablam! | Nov 01 09:42:15.568 INFO kablam! 338 | let mut need_trim:bool; Nov 01 09:42:15.568 INFO kablam! | ----^^^^^^^^^ Nov 01 09:42:15.568 INFO kablam! | | Nov 01 09:42:15.568 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.568 INFO kablam! Nov 01 09:42:15.569 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.569 INFO kablam! --> src/main.rs:355:9 Nov 01 09:42:15.569 INFO kablam! | Nov 01 09:42:15.569 INFO kablam! 355 | let mut chrom = 0; Nov 01 09:42:15.569 INFO kablam! | ----^^^^^ Nov 01 09:42:15.569 INFO kablam! | | Nov 01 09:42:15.569 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.570 INFO kablam! Nov 01 09:42:15.592 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Nov 01 09:42:15.592 INFO kablam! --> src/main.rs:68:1 Nov 01 09:42:15.592 INFO kablam! | Nov 01 09:42:15.592 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Nov 01 09:42:15.592 INFO kablam! 69 | | Nov 01 09:42:15.592 INFO kablam! 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Nov 01 09:42:15.593 INFO kablam! 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Nov 01 09:42:15.593 INFO kablam! ... | Nov 01 09:42:15.593 INFO kablam! 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Nov 01 09:42:15.593 INFO kablam! 98 | | } Nov 01 09:42:15.593 INFO kablam! | |_^ Nov 01 09:42:15.593 INFO kablam! | Nov 01 09:42:15.593 INFO kablam! = note: #[warn(non_snake_case)] on by default Nov 01 09:42:15.593 INFO kablam! Nov 01 09:42:15.593 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Nov 01 09:42:15.593 INFO kablam! --> src/main.rs:147:9 Nov 01 09:42:15.593 INFO kablam! | Nov 01 09:42:15.593 INFO kablam! 147 | let mut baseEach_num_record = String::new(); Nov 01 09:42:15.593 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.593 INFO kablam! Nov 01 09:42:15.593 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Nov 01 09:42:15.593 INFO kablam! --> src/main.rs:148:9 Nov 01 09:42:15.593 INFO kablam! | Nov 01 09:42:15.593 INFO kablam! 148 | let mut baseEach_percent_record = String::new(); Nov 01 09:42:15.594 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.594 INFO kablam! Nov 01 09:42:15.596 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.596 INFO kablam! --> src/main.rs:267:9 Nov 01 09:42:15.596 INFO kablam! | Nov 01 09:42:15.596 INFO kablam! 267 | o_buff.write(&member_record.2); Nov 01 09:42:15.596 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.596 INFO kablam! | Nov 01 09:42:15.596 INFO kablam! = note: #[warn(unused_must_use)] on by default Nov 01 09:42:15.596 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.596 INFO kablam! Nov 01 09:42:15.596 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.596 INFO kablam! --> src/main.rs:269:9 Nov 01 09:42:15.596 INFO kablam! | Nov 01 09:42:15.596 INFO kablam! 269 | o_buff.write(&member_record.0); Nov 01 09:42:15.596 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.596 INFO kablam! | Nov 01 09:42:15.596 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.596 INFO kablam! Nov 01 09:42:15.596 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.596 INFO kablam! --> src/main.rs:272:9 Nov 01 09:42:15.596 INFO kablam! | Nov 01 09:42:15.596 INFO kablam! 272 | o_buff.write(&real_qual_temp); Nov 01 09:42:15.596 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.596 INFO kablam! | Nov 01 09:42:15.596 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.596 INFO kablam! Nov 01 09:42:15.596 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.596 INFO kablam! --> src/main.rs:274:5 Nov 01 09:42:15.596 INFO kablam! | Nov 01 09:42:15.596 INFO kablam! 274 | o_buff.write(b"\n"); Nov 01 09:42:15.596 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.596 INFO kablam! | Nov 01 09:42:15.596 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.596 INFO kablam! Nov 01 09:42:15.599 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.599 INFO kablam! --> src/main.rs:277:5 Nov 01 09:42:15.599 INFO kablam! | Nov 01 09:42:15.599 INFO kablam! 277 | o_buff.write(b"\n"); Nov 01 09:42:15.599 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.599 INFO kablam! | Nov 01 09:42:15.599 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.599 INFO kablam! Nov 01 09:42:15.599 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.600 INFO kablam! --> src/main.rs:280:5 Nov 01 09:42:15.600 INFO kablam! | Nov 01 09:42:15.600 INFO kablam! 280 | o_buff.write(b"\n"); Nov 01 09:42:15.600 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.600 INFO kablam! | Nov 01 09:42:15.600 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.600 INFO kablam! Nov 01 09:42:15.600 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Nov 01 09:42:15.600 INFO kablam! --> src/main.rs:286:10 Nov 01 09:42:15.600 INFO kablam! | Nov 01 09:42:15.600 INFO kablam! 286 | for (key_dupGroup, pair_dup) in pd.iter() { Nov 01 09:42:15.600 INFO kablam! | ^^^^^^^^^^^^ Nov 01 09:42:15.600 INFO kablam! Nov 01 09:42:15.600 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Nov 01 09:42:15.600 INFO kablam! --> src/main.rs:357:9 Nov 01 09:42:15.600 INFO kablam! | Nov 01 09:42:15.600 INFO kablam! 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Nov 01 09:42:15.600 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.600 INFO kablam! Nov 01 09:42:15.600 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Nov 01 09:42:15.600 INFO kablam! --> src/main.rs:387:17 Nov 01 09:42:15.600 INFO kablam! | Nov 01 09:42:15.600 INFO kablam! 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Nov 01 09:42:15.600 INFO kablam! | ^^^^^^^^^^^^ Nov 01 09:42:15.600 INFO kablam! Nov 01 09:42:15.740 INFO kablam! warning: unused import: `std::io::prelude` Nov 01 09:42:15.740 INFO kablam! --> src/main.rs:22:5 Nov 01 09:42:15.740 INFO kablam! | Nov 01 09:42:15.740 INFO kablam! 22 | use std::io::prelude::*; Nov 01 09:42:15.740 INFO kablam! | ^^^^^^^^^^^^^^^^ Nov 01 09:42:15.740 INFO kablam! Nov 01 09:42:15.759 INFO kablam! warning: unused variable: `consensus_base` Nov 01 09:42:15.759 INFO kablam! --> src/main.rs:139:9 Nov 01 09:42:15.760 INFO kablam! | Nov 01 09:42:15.760 INFO kablam! 139 | let consensus_base:Vec = Vec::new(); Nov 01 09:42:15.760 INFO kablam! | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Nov 01 09:42:15.760 INFO kablam! | Nov 01 09:42:15.760 INFO kablam! = note: #[warn(unused_variables)] on by default Nov 01 09:42:15.760 INFO kablam! Nov 01 09:42:15.760 INFO kablam! warning: unused variable: `consensus_source_reads` Nov 01 09:42:15.760 INFO kablam! --> src/main.rs:144:13 Nov 01 09:42:15.760 INFO kablam! | Nov 01 09:42:15.760 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Nov 01 09:42:15.760 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Nov 01 09:42:15.760 INFO kablam! Nov 01 09:42:15.760 INFO kablam! warning: unused variable: `chrom` Nov 01 09:42:15.760 INFO kablam! --> src/main.rs:283:121 Nov 01 09:42:15.760 INFO kablam! | Nov 01 09:42:15.760 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) { Nov 01 09:42:15.760 INFO kablam! | ^^^^^ help: consider using `_chrom` instead Nov 01 09:42:15.760 INFO kablam! Nov 01 09:42:15.760 INFO kablam! warning: value assigned to `new_seq_b` is never read Nov 01 09:42:15.760 INFO kablam! --> src/main.rs:370:21 Nov 01 09:42:15.760 INFO kablam! | Nov 01 09:42:15.760 INFO kablam! 370 | let mut new_seq_b:Vec = Vec::new(); Nov 01 09:42:15.760 INFO kablam! | ^^^^^^^^^ Nov 01 09:42:15.760 INFO kablam! | Nov 01 09:42:15.760 INFO kablam! = note: #[warn(unused_assignments)] on by default Nov 01 09:42:15.760 INFO kablam! Nov 01 09:42:15.777 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.777 INFO kablam! --> src/main.rs:74:9 Nov 01 09:42:15.777 INFO kablam! | Nov 01 09:42:15.777 INFO kablam! 74 | let mut pair; Nov 01 09:42:15.777 INFO kablam! | ----^^^^ Nov 01 09:42:15.777 INFO kablam! | | Nov 01 09:42:15.777 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.777 INFO kablam! | Nov 01 09:42:15.777 INFO kablam! = note: #[warn(unused_mut)] on by default Nov 01 09:42:15.777 INFO kablam! Nov 01 09:42:15.777 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.777 INFO kablam! --> src/main.rs:75:9 Nov 01 09:42:15.777 INFO kablam! | Nov 01 09:42:15.777 INFO kablam! 75 | let mut strand; Nov 01 09:42:15.777 INFO kablam! | ----^^^^^^ Nov 01 09:42:15.777 INFO kablam! | | Nov 01 09:42:15.777 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.777 INFO kablam! Nov 01 09:42:15.777 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.777 INFO kablam! --> src/main.rs:76:9 Nov 01 09:42:15.778 INFO kablam! | Nov 01 09:42:15.778 INFO kablam! 76 | let mut aln_pos; Nov 01 09:42:15.778 INFO kablam! | ----^^^^^^^ Nov 01 09:42:15.778 INFO kablam! | | Nov 01 09:42:15.778 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.778 INFO kablam! Nov 01 09:42:15.816 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.816 INFO kablam! --> src/main.rs:144:9 Nov 01 09:42:15.816 INFO kablam! | Nov 01 09:42:15.816 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Nov 01 09:42:15.816 INFO kablam! | ----^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.816 INFO kablam! | | Nov 01 09:42:15.816 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.816 INFO kablam! Nov 01 09:42:15.816 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.816 INFO kablam! --> src/main.rs:151:9 Nov 01 09:42:15.816 INFO kablam! | Nov 01 09:42:15.816 INFO kablam! 151 | let mut top_cigar:&CigarStringView; Nov 01 09:42:15.816 INFO kablam! | ----^^^^^^^^^ Nov 01 09:42:15.816 INFO kablam! | | Nov 01 09:42:15.816 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.816 INFO kablam! Nov 01 09:42:15.839 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.839 INFO kablam! --> src/main.rs:338:9 Nov 01 09:42:15.839 INFO kablam! | Nov 01 09:42:15.839 INFO kablam! 338 | let mut need_trim:bool; Nov 01 09:42:15.839 INFO kablam! | ----^^^^^^^^^ Nov 01 09:42:15.839 INFO kablam! | | Nov 01 09:42:15.839 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.839 INFO kablam! Nov 01 09:42:15.839 INFO kablam! warning: variable does not need to be mutable Nov 01 09:42:15.839 INFO kablam! --> src/main.rs:355:9 Nov 01 09:42:15.839 INFO kablam! | Nov 01 09:42:15.839 INFO kablam! 355 | let mut chrom = 0; Nov 01 09:42:15.839 INFO kablam! | ----^^^^^ Nov 01 09:42:15.839 INFO kablam! | | Nov 01 09:42:15.839 INFO kablam! | help: remove this `mut` Nov 01 09:42:15.839 INFO kablam! Nov 01 09:42:15.851 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Nov 01 09:42:15.851 INFO kablam! --> src/main.rs:68:1 Nov 01 09:42:15.851 INFO kablam! | Nov 01 09:42:15.851 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Nov 01 09:42:15.851 INFO kablam! 69 | | Nov 01 09:42:15.851 INFO kablam! 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Nov 01 09:42:15.851 INFO kablam! 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Nov 01 09:42:15.851 INFO kablam! ... | Nov 01 09:42:15.851 INFO kablam! 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Nov 01 09:42:15.851 INFO kablam! 98 | | } Nov 01 09:42:15.851 INFO kablam! | |_^ Nov 01 09:42:15.851 INFO kablam! | Nov 01 09:42:15.851 INFO kablam! = note: #[warn(non_snake_case)] on by default Nov 01 09:42:15.851 INFO kablam! Nov 01 09:42:15.851 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Nov 01 09:42:15.851 INFO kablam! --> src/main.rs:147:9 Nov 01 09:42:15.851 INFO kablam! | Nov 01 09:42:15.851 INFO kablam! 147 | let mut baseEach_num_record = String::new(); Nov 01 09:42:15.851 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.851 INFO kablam! Nov 01 09:42:15.851 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Nov 01 09:42:15.851 INFO kablam! --> src/main.rs:148:9 Nov 01 09:42:15.851 INFO kablam! | Nov 01 09:42:15.851 INFO kablam! 148 | let mut baseEach_percent_record = String::new(); Nov 01 09:42:15.851 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.851 INFO kablam! Nov 01 09:42:15.852 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.852 INFO kablam! --> src/main.rs:267:9 Nov 01 09:42:15.852 INFO kablam! | Nov 01 09:42:15.852 INFO kablam! 267 | o_buff.write(&member_record.2); Nov 01 09:42:15.852 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.852 INFO kablam! | Nov 01 09:42:15.852 INFO kablam! = note: #[warn(unused_must_use)] on by default Nov 01 09:42:15.852 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.852 INFO kablam! Nov 01 09:42:15.852 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.852 INFO kablam! --> src/main.rs:269:9 Nov 01 09:42:15.852 INFO kablam! | Nov 01 09:42:15.852 INFO kablam! 269 | o_buff.write(&member_record.0); Nov 01 09:42:15.852 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.852 INFO kablam! | Nov 01 09:42:15.852 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.852 INFO kablam! Nov 01 09:42:15.852 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.852 INFO kablam! --> src/main.rs:272:9 Nov 01 09:42:15.852 INFO kablam! | Nov 01 09:42:15.852 INFO kablam! 272 | o_buff.write(&real_qual_temp); Nov 01 09:42:15.852 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.852 INFO kablam! | Nov 01 09:42:15.852 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.852 INFO kablam! Nov 01 09:42:15.856 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.856 INFO kablam! --> src/main.rs:274:5 Nov 01 09:42:15.856 INFO kablam! | Nov 01 09:42:15.856 INFO kablam! 274 | o_buff.write(b"\n"); Nov 01 09:42:15.856 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.856 INFO kablam! | Nov 01 09:42:15.856 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.856 INFO kablam! Nov 01 09:42:15.856 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.856 INFO kablam! --> src/main.rs:277:5 Nov 01 09:42:15.856 INFO kablam! | Nov 01 09:42:15.856 INFO kablam! 277 | o_buff.write(b"\n"); Nov 01 09:42:15.856 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.856 INFO kablam! | Nov 01 09:42:15.856 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.856 INFO kablam! Nov 01 09:42:15.856 INFO kablam! warning: unused `std::result::Result` that must be used Nov 01 09:42:15.856 INFO kablam! --> src/main.rs:280:5 Nov 01 09:42:15.856 INFO kablam! | Nov 01 09:42:15.856 INFO kablam! 280 | o_buff.write(b"\n"); Nov 01 09:42:15.856 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.856 INFO kablam! | Nov 01 09:42:15.856 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Nov 01 09:42:15.857 INFO kablam! Nov 01 09:42:15.857 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Nov 01 09:42:15.857 INFO kablam! --> src/main.rs:286:10 Nov 01 09:42:15.857 INFO kablam! | Nov 01 09:42:15.857 INFO kablam! 286 | for (key_dupGroup, pair_dup) in pd.iter() { Nov 01 09:42:15.857 INFO kablam! | ^^^^^^^^^^^^ Nov 01 09:42:15.857 INFO kablam! Nov 01 09:42:15.857 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Nov 01 09:42:15.857 INFO kablam! --> src/main.rs:357:9 Nov 01 09:42:15.857 INFO kablam! | Nov 01 09:42:15.857 INFO kablam! 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Nov 01 09:42:15.857 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^ Nov 01 09:42:15.857 INFO kablam! Nov 01 09:42:15.857 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Nov 01 09:42:15.857 INFO kablam! --> src/main.rs:387:17 Nov 01 09:42:15.857 INFO kablam! | Nov 01 09:42:15.857 INFO kablam! 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Nov 01 09:42:15.857 INFO kablam! | ^^^^^^^^^^^^ Nov 01 09:42:15.857 INFO kablam! Nov 01 09:42:15.932 INFO kablam! Finished dev [unoptimized + debuginfo] target(s) in 33.30s Nov 01 09:42:15.941 INFO kablam! su: No module specific data is present Nov 01 09:42:17.648 INFO running `"docker" "rm" "-f" "572c445341b250c9fef4633898f45a280117c08f2875c3eef613da8fb8a7fb85"` Nov 01 09:42:17.952 INFO blam! 572c445341b250c9fef4633898f45a280117c08f2875c3eef613da8fb8a7fb85