Sep 19 16:43:15.123 INFO checking TuBieJun/consensus against master#1e21c9a297a9fe668d62887a3a6a4add8e717b17 for pr-54352 Sep 19 16:43:15.123 INFO running: cargo +1e21c9a297a9fe668d62887a3a6a4add8e717b17-alt check --frozen --all --all-targets Sep 19 16:43:15.123 INFO running `"docker" "create" "-v" "/home/ec2-user/crater/./work/local/test-source/worker-4/pr-54352/master#1e21c9a297a9fe668d62887a3a6a4add8e717b17:/source:ro,Z" "-v" "/home/ec2-user/crater/./work/local/target-dirs/pr-54352/worker-4/master#1e21c9a297a9fe668d62887a3a6a4add8e717b17:/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 +1e21c9a297a9fe668d62887a3a6a4add8e717b17-alt check --frozen --all --all-targets" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-m" "1536M" "crater"` Sep 19 16:43:15.352 INFO blam! ac7d58268ec3c990cd038e015c34950602741971f3706a90a770936702d2ce65 Sep 19 16:43:15.354 INFO running `"docker" "start" "-a" "ac7d58268ec3c990cd038e015c34950602741971f3706a90a770936702d2ce65"` Sep 19 16:43:16.381 INFO kablam! usermod: no changes Sep 19 16:43:16.538 INFO kablam! Checking custom_derive v0.1.7 Sep 19 16:43:16.546 INFO kablam! Checking ieee754 v0.2.2 Sep 19 16:43:16.550 INFO kablam! Compiling fs-utils v1.0.0 Sep 19 16:43:16.550 INFO kablam! Checking itertools v0.6.5 Sep 19 16:43:16.550 INFO kablam! Compiling newtype_derive v0.1.6 Sep 19 16:43:18.422 INFO kablam! Compiling rust-htslib v0.15.0 Sep 19 16:43:48.296 INFO kablam! Checking consensus v0.1.0 (/source) Sep 19 16:43:48.862 INFO kablam! warning: unused import: `std::env` Sep 19 16:43:48.863 INFO kablam! --> src/main.rs:12:5 Sep 19 16:43:48.863 INFO kablam! | Sep 19 16:43:48.863 INFO kablam! 12 | use std::env; Sep 19 16:43:48.864 INFO kablam! | ^^^^^^^^ Sep 19 16:43:48.864 INFO kablam! | Sep 19 16:43:48.864 INFO kablam! = note: #[warn(unused_imports)] on by default Sep 19 16:43:48.865 INFO kablam! Sep 19 16:43:48.865 INFO kablam! warning: unused import: `rust_htslib::prelude::*` Sep 19 16:43:48.866 INFO kablam! --> src/main.rs:16:5 Sep 19 16:43:48.866 INFO kablam! | Sep 19 16:43:48.866 INFO kablam! 16 | use rust_htslib::prelude::*; Sep 19 16:43:48.867 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:48.867 INFO kablam! Sep 19 16:43:48.867 INFO kablam! warning: unused import: `std::io` Sep 19 16:43:48.868 INFO kablam! --> src/main.rs:21:5 Sep 19 16:43:48.868 INFO kablam! | Sep 19 16:43:48.868 INFO kablam! 21 | use std::io; Sep 19 16:43:48.869 INFO kablam! | ^^^^^^^ Sep 19 16:43:48.869 INFO kablam! Sep 19 16:43:48.869 INFO kablam! warning: unused import: `PathBuf` Sep 19 16:43:48.869 INFO kablam! --> src/main.rs:25:23 Sep 19 16:43:48.870 INFO kablam! | Sep 19 16:43:48.870 INFO kablam! 25 | use std::path::{Path, PathBuf}; Sep 19 16:43:48.871 INFO kablam! | ^^^^^^^ Sep 19 16:43:48.871 INFO kablam! Sep 19 16:43:48.871 INFO kablam! warning: unused import: `SubCommand` Sep 19 16:43:48.871 INFO kablam! --> src/main.rs:26:22 Sep 19 16:43:48.872 INFO kablam! | Sep 19 16:43:48.872 INFO kablam! 26 | use clap::{Arg, App, SubCommand}; Sep 19 16:43:48.872 INFO kablam! | ^^^^^^^^^^ Sep 19 16:43:48.873 INFO kablam! Sep 19 16:43:48.873 INFO kablam! warning: unnecessary parentheses around `if` condition Sep 19 16:43:48.873 INFO kablam! --> src/main.rs:218:20 Sep 19 16:43:48.874 INFO kablam! | Sep 19 16:43:48.874 INFO kablam! 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Sep 19 16:43:48.875 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Sep 19 16:43:48.875 INFO kablam! | Sep 19 16:43:48.875 INFO kablam! = note: #[warn(unused_parens)] on by default Sep 19 16:43:48.876 INFO kablam! Sep 19 16:43:48.876 INFO kablam! warning: unnecessary parentheses around `if` condition Sep 19 16:43:48.876 INFO kablam! --> src/main.rs:239:16 Sep 19 16:43:48.877 INFO kablam! | Sep 19 16:43:48.877 INFO kablam! 239 | if (baseEach_percent_record.len() > 0) { Sep 19 16:43:48.878 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Sep 19 16:43:48.878 INFO kablam! Sep 19 16:43:49.035 INFO kablam! warning: unused import: `std::io::prelude` Sep 19 16:43:49.036 INFO kablam! --> src/main.rs:22:5 Sep 19 16:43:49.036 INFO kablam! | Sep 19 16:43:49.037 INFO kablam! 22 | use std::io::prelude::*; Sep 19 16:43:49.037 INFO kablam! | ^^^^^^^^^^^^^^^^ Sep 19 16:43:49.037 INFO kablam! Sep 19 16:43:49.086 INFO kablam! warning: unused variable: `consensus_base` Sep 19 16:43:49.086 INFO kablam! --> src/main.rs:139:9 Sep 19 16:43:49.087 INFO kablam! | Sep 19 16:43:49.087 INFO kablam! 139 | let consensus_base:Vec = Vec::new(); Sep 19 16:43:49.088 INFO kablam! | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Sep 19 16:43:49.088 INFO kablam! | Sep 19 16:43:49.088 INFO kablam! = note: #[warn(unused_variables)] on by default Sep 19 16:43:49.089 INFO kablam! warning: unused import: `std::env` Sep 19 16:43:49.089 INFO kablam! --> src/main.rs:12:5 Sep 19 16:43:49.090 INFO kablam! | Sep 19 16:43:49.090 INFO kablam! 12 | use std::env; Sep 19 16:43:49.090 INFO kablam! | ^^^^^^^^ Sep 19 16:43:49.091 INFO kablam! | Sep 19 16:43:49.091 INFO kablam! = note: #[warn(unused_imports)] on by default Sep 19 16:43:49.091 INFO kablam! Sep 19 16:43:49.092 INFO kablam! warning: unused import: `rust_htslib::prelude::*` Sep 19 16:43:49.092 INFO kablam! --> src/main.rs:16:5 Sep 19 16:43:49.092 INFO kablam! | Sep 19 16:43:49.093 INFO kablam! 16 | use rust_htslib::prelude::*; Sep 19 16:43:49.093 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.093 INFO kablam! Sep 19 16:43:49.094 INFO kablam! warning: unused import: `std::io` Sep 19 16:43:49.094 INFO kablam! --> src/main.rs:21:5 Sep 19 16:43:49.094 INFO kablam! | Sep 19 16:43:49.095 INFO kablam! 21 | use std::io; Sep 19 16:43:49.095 INFO kablam! | ^^^^^^^ Sep 19 16:43:49.095 INFO kablam! Sep 19 16:43:49.096 INFO kablam! warning: unused import: `PathBuf` Sep 19 16:43:49.096 INFO kablam! --> src/main.rs:25:23 Sep 19 16:43:49.097 INFO kablam! | Sep 19 16:43:49.097 INFO kablam! 25 | use std::path::{Path, PathBuf}; Sep 19 16:43:49.097 INFO kablam! | ^^^^^^^ Sep 19 16:43:49.098 INFO kablam! Sep 19 16:43:49.098 INFO kablam! warning: unused import: `SubCommand` Sep 19 16:43:49.098 INFO kablam! --> src/main.rs:26:22 Sep 19 16:43:49.099 INFO kablam! | Sep 19 16:43:49.099 INFO kablam! 26 | use clap::{Arg, App, SubCommand}; Sep 19 16:43:49.099 INFO kablam! | ^^^^^^^^^^ Sep 19 16:43:49.100 INFO kablam! Sep 19 16:43:49.100 INFO kablam! warning: unnecessary parentheses around `if` condition Sep 19 16:43:49.100 INFO kablam! --> src/main.rs:218:20 Sep 19 16:43:49.101 INFO kablam! | Sep 19 16:43:49.101 INFO kablam! 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Sep 19 16:43:49.101 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Sep 19 16:43:49.102 INFO kablam! | Sep 19 16:43:49.102 INFO kablam! = note: #[warn(unused_parens)] on by default Sep 19 16:43:49.102 INFO kablam! Sep 19 16:43:49.103 INFO kablam! warning: unnecessary parentheses around `if` condition Sep 19 16:43:49.103 INFO kablam! --> src/main.rs:239:16 Sep 19 16:43:49.103 INFO kablam! | Sep 19 16:43:49.103 INFO kablam! 239 | if (baseEach_percent_record.len() > 0) { Sep 19 16:43:49.104 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Sep 19 16:43:49.104 INFO kablam! Sep 19 16:43:49.104 INFO kablam! Sep 19 16:43:49.105 INFO kablam! warning: unused variable: `consensus_source_reads` Sep 19 16:43:49.105 INFO kablam! --> src/main.rs:144:13 Sep 19 16:43:49.105 INFO kablam! | Sep 19 16:43:49.106 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Sep 19 16:43:49.106 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Sep 19 16:43:49.106 INFO kablam! Sep 19 16:43:49.107 INFO kablam! warning: unused variable: `chrom` Sep 19 16:43:49.107 INFO kablam! --> src/main.rs:283:121 Sep 19 16:43:49.107 INFO kablam! | Sep 19 16:43:49.108 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 19 16:43:49.108 INFO kablam! | ^^^^^ help: consider using `_chrom` instead Sep 19 16:43:49.109 INFO kablam! Sep 19 16:43:49.109 INFO kablam! warning: value assigned to `new_seq_b` is never read Sep 19 16:43:49.109 INFO kablam! --> src/main.rs:370:21 Sep 19 16:43:49.110 INFO kablam! | Sep 19 16:43:49.110 INFO kablam! 370 | let mut new_seq_b:Vec = Vec::new(); Sep 19 16:43:49.111 INFO kablam! | ^^^^^^^^^ Sep 19 16:43:49.118 INFO kablam! | Sep 19 16:43:49.118 INFO kablam! = note: #[warn(unused_assignments)] on by default Sep 19 16:43:49.119 INFO kablam! Sep 19 16:43:49.119 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.119 INFO kablam! --> src/main.rs:74:9 Sep 19 16:43:49.120 INFO kablam! | Sep 19 16:43:49.120 INFO kablam! 74 | let mut pair; Sep 19 16:43:49.120 INFO kablam! | ----^^^^ Sep 19 16:43:49.121 INFO kablam! | | Sep 19 16:43:49.121 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.122 INFO kablam! | Sep 19 16:43:49.122 INFO kablam! = note: #[warn(unused_mut)] on by default Sep 19 16:43:49.122 INFO kablam! Sep 19 16:43:49.123 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.123 INFO kablam! --> src/main.rs:75:9 Sep 19 16:43:49.123 INFO kablam! | Sep 19 16:43:49.124 INFO kablam! 75 | let mut strand; Sep 19 16:43:49.124 INFO kablam! | ----^^^^^^ Sep 19 16:43:49.124 INFO kablam! | | Sep 19 16:43:49.124 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.125 INFO kablam! Sep 19 16:43:49.125 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.125 INFO kablam! --> src/main.rs:76:9 Sep 19 16:43:49.126 INFO kablam! | Sep 19 16:43:49.126 INFO kablam! 76 | let mut aln_pos; Sep 19 16:43:49.126 INFO kablam! | ----^^^^^^^ Sep 19 16:43:49.127 INFO kablam! | | Sep 19 16:43:49.127 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.127 INFO kablam! Sep 19 16:43:49.184 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.185 INFO kablam! --> src/main.rs:144:9 Sep 19 16:43:49.185 INFO kablam! | Sep 19 16:43:49.185 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Sep 19 16:43:49.186 INFO kablam! | ----^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.186 INFO kablam! | | Sep 19 16:43:49.186 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.187 INFO kablam! Sep 19 16:43:49.187 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.187 INFO kablam! --> src/main.rs:151:9 Sep 19 16:43:49.188 INFO kablam! | Sep 19 16:43:49.188 INFO kablam! 151 | let mut top_cigar:&CigarStringView; Sep 19 16:43:49.188 INFO kablam! | ----^^^^^^^^^ Sep 19 16:43:49.189 INFO kablam! | | Sep 19 16:43:49.189 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.189 INFO kablam! Sep 19 16:43:49.218 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.218 INFO kablam! --> src/main.rs:338:9 Sep 19 16:43:49.218 INFO kablam! | Sep 19 16:43:49.219 INFO kablam! 338 | let mut need_trim:bool; Sep 19 16:43:49.219 INFO kablam! | ----^^^^^^^^^ Sep 19 16:43:49.220 INFO kablam! | | Sep 19 16:43:49.220 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.220 INFO kablam! Sep 19 16:43:49.221 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.221 INFO kablam! --> src/main.rs:355:9 Sep 19 16:43:49.222 INFO kablam! | Sep 19 16:43:49.222 INFO kablam! 355 | let mut chrom = 0; Sep 19 16:43:49.222 INFO kablam! | ----^^^^^ Sep 19 16:43:49.223 INFO kablam! | | Sep 19 16:43:49.223 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.224 INFO kablam! Sep 19 16:43:49.227 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Sep 19 16:43:49.227 INFO kablam! --> src/main.rs:68:1 Sep 19 16:43:49.227 INFO kablam! | Sep 19 16:43:49.228 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Sep 19 16:43:49.228 INFO kablam! 69 | | Sep 19 16:43:49.229 INFO kablam! 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Sep 19 16:43:49.229 INFO kablam! 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Sep 19 16:43:49.229 INFO kablam! ... | Sep 19 16:43:49.230 INFO kablam! 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Sep 19 16:43:49.230 INFO kablam! 98 | | } Sep 19 16:43:49.231 INFO kablam! | |_^ Sep 19 16:43:49.231 INFO kablam! | Sep 19 16:43:49.232 INFO kablam! = note: #[warn(non_snake_case)] on by default Sep 19 16:43:49.232 INFO kablam! Sep 19 16:43:49.232 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Sep 19 16:43:49.233 INFO kablam! --> src/main.rs:147:9 Sep 19 16:43:49.233 INFO kablam! | Sep 19 16:43:49.233 INFO kablam! 147 | let mut baseEach_num_record = String::new(); Sep 19 16:43:49.234 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.234 INFO kablam! Sep 19 16:43:49.235 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Sep 19 16:43:49.235 INFO kablam! --> src/main.rs:148:9 Sep 19 16:43:49.235 INFO kablam! | Sep 19 16:43:49.236 INFO kablam! 148 | let mut baseEach_percent_record = String::new(); Sep 19 16:43:49.236 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.237 INFO kablam! Sep 19 16:43:49.237 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.237 INFO kablam! --> src/main.rs:267:9 Sep 19 16:43:49.238 INFO kablam! | Sep 19 16:43:49.238 INFO kablam! 267 | o_buff.write(&member_record.2); Sep 19 16:43:49.239 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.239 INFO kablam! | Sep 19 16:43:49.239 INFO kablam! = note: #[warn(unused_must_use)] on by default Sep 19 16:43:49.240 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.240 INFO kablam! Sep 19 16:43:49.240 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.241 INFO kablam! --> src/main.rs:269:9 Sep 19 16:43:49.241 INFO kablam! | Sep 19 16:43:49.242 INFO kablam! 269 | o_buff.write(&member_record.0); Sep 19 16:43:49.242 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.243 INFO kablam! | Sep 19 16:43:49.243 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.243 INFO kablam! Sep 19 16:43:49.244 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.244 INFO kablam! --> src/main.rs:272:9 Sep 19 16:43:49.244 INFO kablam! | Sep 19 16:43:49.245 INFO kablam! 272 | o_buff.write(&real_qual_temp); Sep 19 16:43:49.245 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.246 INFO kablam! | Sep 19 16:43:49.246 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.246 INFO kablam! Sep 19 16:43:49.247 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.247 INFO kablam! --> src/main.rs:274:5 Sep 19 16:43:49.248 INFO kablam! | Sep 19 16:43:49.248 INFO kablam! 274 | o_buff.write(b"\n"); Sep 19 16:43:49.248 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.249 INFO kablam! | Sep 19 16:43:49.249 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.249 INFO kablam! Sep 19 16:43:49.250 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.250 INFO kablam! --> src/main.rs:277:5 Sep 19 16:43:49.251 INFO kablam! | Sep 19 16:43:49.251 INFO kablam! 277 | o_buff.write(b"\n"); Sep 19 16:43:49.252 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.252 INFO kablam! | Sep 19 16:43:49.252 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.253 INFO kablam! Sep 19 16:43:49.253 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.254 INFO kablam! --> src/main.rs:280:5 Sep 19 16:43:49.254 INFO kablam! | Sep 19 16:43:49.254 INFO kablam! 280 | o_buff.write(b"\n"); Sep 19 16:43:49.255 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.255 INFO kablam! | Sep 19 16:43:49.255 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.256 INFO kablam! Sep 19 16:43:49.256 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Sep 19 16:43:49.257 INFO kablam! --> src/main.rs:286:10 Sep 19 16:43:49.257 INFO kablam! | Sep 19 16:43:49.257 INFO kablam! 286 | for (key_dupGroup, pair_dup) in pd.iter() { Sep 19 16:43:49.258 INFO kablam! | ^^^^^^^^^^^^ Sep 19 16:43:49.258 INFO kablam! Sep 19 16:43:49.258 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Sep 19 16:43:49.259 INFO kablam! --> src/main.rs:357:9 Sep 19 16:43:49.259 INFO kablam! | Sep 19 16:43:49.260 INFO kablam! 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Sep 19 16:43:49.260 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.260 INFO kablam! Sep 19 16:43:49.261 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Sep 19 16:43:49.261 INFO kablam! --> src/main.rs:387:17 Sep 19 16:43:49.261 INFO kablam! | Sep 19 16:43:49.262 INFO kablam! 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Sep 19 16:43:49.262 INFO kablam! | ^^^^^^^^^^^^ Sep 19 16:43:49.262 INFO kablam! Sep 19 16:43:49.310 INFO kablam! warning: unused import: `std::io::prelude` Sep 19 16:43:49.311 INFO kablam! --> src/main.rs:22:5 Sep 19 16:43:49.311 INFO kablam! | Sep 19 16:43:49.312 INFO kablam! 22 | use std::io::prelude::*; Sep 19 16:43:49.312 INFO kablam! | ^^^^^^^^^^^^^^^^ Sep 19 16:43:49.312 INFO kablam! Sep 19 16:43:49.345 INFO kablam! warning: unused variable: `consensus_base` Sep 19 16:43:49.346 INFO kablam! --> src/main.rs:139:9 Sep 19 16:43:49.346 INFO kablam! | Sep 19 16:43:49.346 INFO kablam! 139 | let consensus_base:Vec = Vec::new(); Sep 19 16:43:49.347 INFO kablam! | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Sep 19 16:43:49.347 INFO kablam! | Sep 19 16:43:49.348 INFO kablam! = note: #[warn(unused_variables)] on by default Sep 19 16:43:49.348 INFO kablam! Sep 19 16:43:49.348 INFO kablam! warning: unused variable: `consensus_source_reads` Sep 19 16:43:49.349 INFO kablam! --> src/main.rs:144:13 Sep 19 16:43:49.349 INFO kablam! | Sep 19 16:43:49.349 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Sep 19 16:43:49.350 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Sep 19 16:43:49.350 INFO kablam! Sep 19 16:43:49.350 INFO kablam! warning: unused variable: `chrom` Sep 19 16:43:49.351 INFO kablam! --> src/main.rs:283:121 Sep 19 16:43:49.351 INFO kablam! | Sep 19 16:43:49.352 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 19 16:43:49.352 INFO kablam! | ^^^^^ help: consider using `_chrom` instead Sep 19 16:43:49.352 INFO kablam! Sep 19 16:43:49.352 INFO kablam! warning: value assigned to `new_seq_b` is never read Sep 19 16:43:49.353 INFO kablam! --> src/main.rs:370:21 Sep 19 16:43:49.353 INFO kablam! | Sep 19 16:43:49.354 INFO kablam! 370 | let mut new_seq_b:Vec = Vec::new(); Sep 19 16:43:49.354 INFO kablam! | ^^^^^^^^^ Sep 19 16:43:49.354 INFO kablam! | Sep 19 16:43:49.355 INFO kablam! = note: #[warn(unused_assignments)] on by default Sep 19 16:43:49.355 INFO kablam! Sep 19 16:43:49.355 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.356 INFO kablam! --> src/main.rs:74:9 Sep 19 16:43:49.356 INFO kablam! | Sep 19 16:43:49.356 INFO kablam! 74 | let mut pair; Sep 19 16:43:49.357 INFO kablam! | ----^^^^ Sep 19 16:43:49.357 INFO kablam! | | Sep 19 16:43:49.357 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.358 INFO kablam! | Sep 19 16:43:49.358 INFO kablam! = note: #[warn(unused_mut)] on by default Sep 19 16:43:49.358 INFO kablam! Sep 19 16:43:49.359 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.359 INFO kablam! --> src/main.rs:75:9 Sep 19 16:43:49.359 INFO kablam! | Sep 19 16:43:49.359 INFO kablam! 75 | let mut strand; Sep 19 16:43:49.360 INFO kablam! | ----^^^^^^ Sep 19 16:43:49.360 INFO kablam! | | Sep 19 16:43:49.360 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.360 INFO kablam! Sep 19 16:43:49.361 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.361 INFO kablam! --> src/main.rs:76:9 Sep 19 16:43:49.361 INFO kablam! | Sep 19 16:43:49.361 INFO kablam! 76 | let mut aln_pos; Sep 19 16:43:49.362 INFO kablam! | ----^^^^^^^ Sep 19 16:43:49.362 INFO kablam! | | Sep 19 16:43:49.363 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.363 INFO kablam! Sep 19 16:43:49.386 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.386 INFO kablam! --> src/main.rs:144:9 Sep 19 16:43:49.387 INFO kablam! | Sep 19 16:43:49.387 INFO kablam! 144 | let mut consensus_source_reads = String::new(); Sep 19 16:43:49.387 INFO kablam! | ----^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.388 INFO kablam! | | Sep 19 16:43:49.388 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.388 INFO kablam! Sep 19 16:43:49.389 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.389 INFO kablam! --> src/main.rs:151:9 Sep 19 16:43:49.389 INFO kablam! | Sep 19 16:43:49.390 INFO kablam! 151 | let mut top_cigar:&CigarStringView; Sep 19 16:43:49.390 INFO kablam! | ----^^^^^^^^^ Sep 19 16:43:49.390 INFO kablam! | | Sep 19 16:43:49.391 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.391 INFO kablam! Sep 19 16:43:49.403 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.403 INFO kablam! --> src/main.rs:338:9 Sep 19 16:43:49.403 INFO kablam! | Sep 19 16:43:49.404 INFO kablam! 338 | let mut need_trim:bool; Sep 19 16:43:49.404 INFO kablam! | ----^^^^^^^^^ Sep 19 16:43:49.404 INFO kablam! | | Sep 19 16:43:49.405 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.405 INFO kablam! Sep 19 16:43:49.405 INFO kablam! warning: variable does not need to be mutable Sep 19 16:43:49.405 INFO kablam! --> src/main.rs:355:9 Sep 19 16:43:49.406 INFO kablam! | Sep 19 16:43:49.406 INFO kablam! 355 | let mut chrom = 0; Sep 19 16:43:49.406 INFO kablam! | ----^^^^^ Sep 19 16:43:49.407 INFO kablam! | | Sep 19 16:43:49.407 INFO kablam! | help: remove this `mut` Sep 19 16:43:49.407 INFO kablam! Sep 19 16:43:49.408 INFO kablam! warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Sep 19 16:43:49.408 INFO kablam! --> src/main.rs:68:1 Sep 19 16:43:49.408 INFO kablam! | Sep 19 16:43:49.409 INFO kablam! 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Sep 19 16:43:49.409 INFO kablam! 69 | | Sep 19 16:43:49.409 INFO kablam! 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Sep 19 16:43:49.410 INFO kablam! 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Sep 19 16:43:49.410 INFO kablam! ... | Sep 19 16:43:49.411 INFO kablam! 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Sep 19 16:43:49.411 INFO kablam! 98 | | } Sep 19 16:43:49.411 INFO kablam! | |_^ Sep 19 16:43:49.412 INFO kablam! | Sep 19 16:43:49.412 INFO kablam! = note: #[warn(non_snake_case)] on by default Sep 19 16:43:49.412 INFO kablam! Sep 19 16:43:49.412 INFO kablam! warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Sep 19 16:43:49.413 INFO kablam! --> src/main.rs:147:9 Sep 19 16:43:49.413 INFO kablam! | Sep 19 16:43:49.414 INFO kablam! 147 | let mut baseEach_num_record = String::new(); Sep 19 16:43:49.414 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.414 INFO kablam! Sep 19 16:43:49.414 INFO kablam! warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Sep 19 16:43:49.415 INFO kablam! --> src/main.rs:148:9 Sep 19 16:43:49.415 INFO kablam! | Sep 19 16:43:49.416 INFO kablam! 148 | let mut baseEach_percent_record = String::new(); Sep 19 16:43:49.416 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.416 INFO kablam! Sep 19 16:43:49.416 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.417 INFO kablam! --> src/main.rs:267:9 Sep 19 16:43:49.417 INFO kablam! | Sep 19 16:43:49.418 INFO kablam! 267 | o_buff.write(&member_record.2); Sep 19 16:43:49.418 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.418 INFO kablam! | Sep 19 16:43:49.419 INFO kablam! = note: #[warn(unused_must_use)] on by default Sep 19 16:43:49.419 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.419 INFO kablam! Sep 19 16:43:49.419 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.420 INFO kablam! --> src/main.rs:269:9 Sep 19 16:43:49.420 INFO kablam! | Sep 19 16:43:49.420 INFO kablam! 269 | o_buff.write(&member_record.0); Sep 19 16:43:49.421 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.421 INFO kablam! | Sep 19 16:43:49.421 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.421 INFO kablam! Sep 19 16:43:49.422 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.422 INFO kablam! --> src/main.rs:272:9 Sep 19 16:43:49.422 INFO kablam! | Sep 19 16:43:49.423 INFO kablam! 272 | o_buff.write(&real_qual_temp); Sep 19 16:43:49.423 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.423 INFO kablam! | Sep 19 16:43:49.424 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.424 INFO kablam! Sep 19 16:43:49.424 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.424 INFO kablam! --> src/main.rs:274:5 Sep 19 16:43:49.425 INFO kablam! | Sep 19 16:43:49.425 INFO kablam! 274 | o_buff.write(b"\n"); Sep 19 16:43:49.426 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.426 INFO kablam! | Sep 19 16:43:49.426 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.427 INFO kablam! Sep 19 16:43:49.427 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.427 INFO kablam! --> src/main.rs:277:5 Sep 19 16:43:49.428 INFO kablam! | Sep 19 16:43:49.428 INFO kablam! 277 | o_buff.write(b"\n"); Sep 19 16:43:49.428 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.429 INFO kablam! | Sep 19 16:43:49.429 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.429 INFO kablam! Sep 19 16:43:49.430 INFO kablam! warning: unused `std::result::Result` which must be used Sep 19 16:43:49.430 INFO kablam! --> src/main.rs:280:5 Sep 19 16:43:49.430 INFO kablam! | Sep 19 16:43:49.431 INFO kablam! 280 | o_buff.write(b"\n"); Sep 19 16:43:49.431 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.431 INFO kablam! | Sep 19 16:43:49.431 INFO kablam! = note: this `Result` may be an `Err` variant, which should be handled Sep 19 16:43:49.432 INFO kablam! Sep 19 16:43:49.432 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Sep 19 16:43:49.432 INFO kablam! --> src/main.rs:286:10 Sep 19 16:43:49.432 INFO kablam! | Sep 19 16:43:49.433 INFO kablam! 286 | for (key_dupGroup, pair_dup) in pd.iter() { Sep 19 16:43:49.433 INFO kablam! | ^^^^^^^^^^^^ Sep 19 16:43:49.433 INFO kablam! Sep 19 16:43:49.433 INFO kablam! warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Sep 19 16:43:49.434 INFO kablam! --> src/main.rs:357:9 Sep 19 16:43:49.434 INFO kablam! | Sep 19 16:43:49.434 INFO kablam! 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Sep 19 16:43:49.435 INFO kablam! | ^^^^^^^^^^^^^^^^^^^^^ Sep 19 16:43:49.435 INFO kablam! Sep 19 16:43:49.435 INFO kablam! warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Sep 19 16:43:49.435 INFO kablam! --> src/main.rs:387:17 Sep 19 16:43:49.436 INFO kablam! | Sep 19 16:43:49.436 INFO kablam! 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Sep 19 16:43:49.436 INFO kablam! | ^^^^^^^^^^^^ Sep 19 16:43:49.436 INFO kablam! Sep 19 16:43:49.451 INFO kablam! Finished dev [unoptimized + debuginfo] target(s) in 33.04s Sep 19 16:43:49.456 INFO kablam! su: No module specific data is present Sep 19 16:43:51.094 INFO running `"docker" "rm" "-f" "ac7d58268ec3c990cd038e015c34950602741971f3706a90a770936702d2ce65"` Sep 19 16:43:51.208 INFO blam! ac7d58268ec3c990cd038e015c34950602741971f3706a90a770936702d2ce65