Dec 11 23:50:13.763 INFO checking TuBieJun/consensus against try#aa9aa79c3c583aab59ac9134542d60a780c35e2e for pr-56677 Dec 11 23:50:13.764 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56677/worker-1/try#aa9aa79c3c583aab59ac9134542d60a780c35e2e:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-1/pr-56677/try#aa9aa79c3c583aab59ac9134542d60a780c35e2e:/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 +aa9aa79c3c583aab59ac9134542d60a780c35e2e-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"` Dec 11 23:50:14.426 INFO [stdout] 276a367bf9406fd63a0dd96728bfefefb6b61fe8bffdbb3373106728f0af6b45 Dec 11 23:50:14.428 INFO running `"docker" "start" "-a" "276a367bf9406fd63a0dd96728bfefefb6b61fe8bffdbb3373106728f0af6b45"` Dec 11 23:50:16.223 INFO [stderr] usermod: no changes Dec 11 23:50:16.353 INFO [stderr] Compiling quick-error v1.2.1 Dec 11 23:50:16.354 INFO [stderr] Checking ieee754 v0.2.2 Dec 11 23:50:16.354 INFO [stderr] Checking itertools v0.6.5 Dec 11 23:50:17.504 INFO [stderr] Compiling fs-utils v1.0.0 Dec 11 23:50:19.121 INFO [stderr] Compiling rust-htslib v0.15.0 Dec 11 23:50:48.314 INFO [stderr] Checking consensus v0.1.0 (/source) Dec 11 23:50:50.924 INFO [stderr] warning: unused import: `std::env` Dec 11 23:50:50.925 INFO [stderr] --> src/main.rs:12:5 Dec 11 23:50:50.925 INFO [stderr] | Dec 11 23:50:50.925 INFO [stderr] 12 | use std::env; Dec 11 23:50:50.925 INFO [stderr] | ^^^^^^^^ Dec 11 23:50:50.925 INFO [stderr] | Dec 11 23:50:50.925 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 11 23:50:50.925 INFO [stderr] Dec 11 23:50:50.925 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 11 23:50:50.925 INFO [stderr] --> src/main.rs:16:5 Dec 11 23:50:50.925 INFO [stderr] | Dec 11 23:50:50.925 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 11 23:50:50.925 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:50.925 INFO [stderr] Dec 11 23:50:50.925 INFO [stderr] warning: unused import: `std::io` Dec 11 23:50:50.925 INFO [stderr] --> src/main.rs:21:5 Dec 11 23:50:50.925 INFO [stderr] | Dec 11 23:50:50.925 INFO [stderr] 21 | use std::io; Dec 11 23:50:50.925 INFO [stderr] | ^^^^^^^ Dec 11 23:50:50.925 INFO [stderr] Dec 11 23:50:50.925 INFO [stderr] warning: unused import: `PathBuf` Dec 11 23:50:50.925 INFO [stderr] --> src/main.rs:25:23 Dec 11 23:50:50.925 INFO [stderr] | Dec 11 23:50:50.925 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 11 23:50:50.925 INFO [stderr] | ^^^^^^^ Dec 11 23:50:50.925 INFO [stderr] Dec 11 23:50:50.925 INFO [stderr] warning: unused import: `SubCommand` Dec 11 23:50:50.925 INFO [stderr] --> src/main.rs:26:22 Dec 11 23:50:50.925 INFO [stderr] | Dec 11 23:50:50.925 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 11 23:50:50.925 INFO [stderr] | ^^^^^^^^^^ Dec 11 23:50:50.925 INFO [stderr] Dec 11 23:50:50.925 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 11 23:50:50.925 INFO [stderr] --> src/main.rs:218:20 Dec 11 23:50:50.925 INFO [stderr] | Dec 11 23:50:50.925 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 11 23:50:50.925 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 11 23:50:50.925 INFO [stderr] | Dec 11 23:50:50.925 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 11 23:50:50.925 INFO [stderr] Dec 11 23:50:50.925 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 11 23:50:50.925 INFO [stderr] --> src/main.rs:239:16 Dec 11 23:50:50.925 INFO [stderr] | Dec 11 23:50:50.925 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 11 23:50:50.925 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 11 23:50:50.925 INFO [stderr] Dec 11 23:50:51.147 INFO [stderr] warning: unused import: `std::io::prelude` Dec 11 23:50:51.147 INFO [stderr] --> src/main.rs:22:5 Dec 11 23:50:51.147 INFO [stderr] | Dec 11 23:50:51.147 INFO [stderr] 22 | use std::io::prelude::*; Dec 11 23:50:51.148 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 11 23:50:51.148 INFO [stderr] Dec 11 23:50:51.174 INFO [stderr] warning: unused variable: `consensus_base` Dec 11 23:50:51.174 INFO [stderr] --> src/main.rs:139:9 Dec 11 23:50:51.174 INFO [stderr] | Dec 11 23:50:51.174 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 11 23:50:51.175 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 11 23:50:51.175 INFO [stderr] | Dec 11 23:50:51.175 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 11 23:50:51.176 INFO [stderr] Dec 11 23:50:51.176 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 11 23:50:51.176 INFO [stderr] --> src/main.rs:144:13 Dec 11 23:50:51.176 INFO [stderr] | Dec 11 23:50:51.177 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 11 23:50:51.177 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 11 23:50:51.177 INFO [stderr] Dec 11 23:50:51.177 INFO [stderr] warning: unused variable: `chrom` Dec 11 23:50:51.178 INFO [stderr] --> src/main.rs:283:121 Dec 11 23:50:51.178 INFO [stderr] | Dec 11 23:50:51.178 INFO [stderr] 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) { Dec 11 23:50:51.178 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 11 23:50:51.178 INFO [stderr] Dec 11 23:50:51.179 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 11 23:50:51.179 INFO [stderr] --> src/main.rs:370:21 Dec 11 23:50:51.179 INFO [stderr] | Dec 11 23:50:51.179 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 11 23:50:51.180 INFO [stderr] | ^^^^^^^^^ Dec 11 23:50:51.180 INFO [stderr] | Dec 11 23:50:51.180 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 11 23:50:51.180 INFO [stderr] Dec 11 23:50:51.181 INFO [stderr] warning: unused import: `std::env` Dec 11 23:50:51.181 INFO [stderr] --> src/main.rs:12:5 Dec 11 23:50:51.181 INFO [stderr] | Dec 11 23:50:51.181 INFO [stderr] 12 | use std::env; Dec 11 23:50:51.182 INFO [stderr] | ^^^^^^^^ Dec 11 23:50:51.182 INFO [stderr] | Dec 11 23:50:51.182 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 11 23:50:51.182 INFO [stderr] Dec 11 23:50:51.182 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 11 23:50:51.183 INFO [stderr] --> src/main.rs:16:5 Dec 11 23:50:51.183 INFO [stderr] | Dec 11 23:50:51.183 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 11 23:50:51.183 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.183 INFO [stderr] Dec 11 23:50:51.184 INFO [stderr] warning: unused import: `std::io` Dec 11 23:50:51.184 INFO [stderr] --> src/main.rs:21:5 Dec 11 23:50:51.184 INFO [stderr] | Dec 11 23:50:51.184 INFO [stderr] 21 | use std::io; Dec 11 23:50:51.185 INFO [stderr] | ^^^^^^^ Dec 11 23:50:51.185 INFO [stderr] Dec 11 23:50:51.185 INFO [stderr] warning: unused import: `PathBuf` Dec 11 23:50:51.185 INFO [stderr] --> src/main.rs:25:23 Dec 11 23:50:51.185 INFO [stderr] | Dec 11 23:50:51.186 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 11 23:50:51.186 INFO [stderr] | ^^^^^^^ Dec 11 23:50:51.186 INFO [stderr] Dec 11 23:50:51.186 INFO [stderr] warning: unused import: `SubCommand` Dec 11 23:50:51.186 INFO [stderr] --> src/main.rs:26:22 Dec 11 23:50:51.187 INFO [stderr] | Dec 11 23:50:51.187 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 11 23:50:51.187 INFO [stderr] | ^^^^^^^^^^ Dec 11 23:50:51.187 INFO [stderr] Dec 11 23:50:51.187 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 11 23:50:51.188 INFO [stderr] --> src/main.rs:218:20 Dec 11 23:50:51.188 INFO [stderr] | Dec 11 23:50:51.188 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 11 23:50:51.188 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 11 23:50:51.188 INFO [stderr] | Dec 11 23:50:51.189 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 11 23:50:51.189 INFO [stderr] Dec 11 23:50:51.189 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 11 23:50:51.189 INFO [stderr] --> src/main.rs:239:16 Dec 11 23:50:51.189 INFO [stderr] | Dec 11 23:50:51.190 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 11 23:50:51.190 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 11 23:50:51.190 INFO [stderr] Dec 11 23:50:51.198 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.198 INFO [stderr] --> src/main.rs:74:9 Dec 11 23:50:51.198 INFO [stderr] | Dec 11 23:50:51.198 INFO [stderr] 74 | let mut pair; Dec 11 23:50:51.199 INFO [stderr] | ----^^^^ Dec 11 23:50:51.199 INFO [stderr] | | Dec 11 23:50:51.199 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.199 INFO [stderr] | Dec 11 23:50:51.200 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 11 23:50:51.200 INFO [stderr] Dec 11 23:50:51.200 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.200 INFO [stderr] --> src/main.rs:75:9 Dec 11 23:50:51.201 INFO [stderr] | Dec 11 23:50:51.201 INFO [stderr] 75 | let mut strand; Dec 11 23:50:51.201 INFO [stderr] | ----^^^^^^ Dec 11 23:50:51.201 INFO [stderr] | | Dec 11 23:50:51.202 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.202 INFO [stderr] Dec 11 23:50:51.202 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.202 INFO [stderr] --> src/main.rs:76:9 Dec 11 23:50:51.203 INFO [stderr] | Dec 11 23:50:51.203 INFO [stderr] 76 | let mut aln_pos; Dec 11 23:50:51.203 INFO [stderr] | ----^^^^^^^ Dec 11 23:50:51.203 INFO [stderr] | | Dec 11 23:50:51.204 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.204 INFO [stderr] Dec 11 23:50:51.252 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.252 INFO [stderr] --> src/main.rs:144:9 Dec 11 23:50:51.253 INFO [stderr] | Dec 11 23:50:51.253 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 11 23:50:51.253 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.253 INFO [stderr] | | Dec 11 23:50:51.253 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.254 INFO [stderr] Dec 11 23:50:51.254 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.254 INFO [stderr] --> src/main.rs:151:9 Dec 11 23:50:51.254 INFO [stderr] | Dec 11 23:50:51.255 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 11 23:50:51.255 INFO [stderr] | ----^^^^^^^^^ Dec 11 23:50:51.255 INFO [stderr] | | Dec 11 23:50:51.255 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.255 INFO [stderr] Dec 11 23:50:51.272 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.272 INFO [stderr] --> src/main.rs:338:9 Dec 11 23:50:51.273 INFO [stderr] | Dec 11 23:50:51.273 INFO [stderr] 338 | let mut need_trim:bool; Dec 11 23:50:51.273 INFO [stderr] | ----^^^^^^^^^ Dec 11 23:50:51.273 INFO [stderr] | | Dec 11 23:50:51.274 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.274 INFO [stderr] Dec 11 23:50:51.274 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.274 INFO [stderr] --> src/main.rs:355:9 Dec 11 23:50:51.274 INFO [stderr] | Dec 11 23:50:51.275 INFO [stderr] 355 | let mut chrom = 0; Dec 11 23:50:51.275 INFO [stderr] | ----^^^^^ Dec 11 23:50:51.275 INFO [stderr] | | Dec 11 23:50:51.288 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.288 INFO [stderr] Dec 11 23:50:51.320 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 11 23:50:51.320 INFO [stderr] --> src/main.rs:68:1 Dec 11 23:50:51.321 INFO [stderr] | Dec 11 23:50:51.321 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 11 23:50:51.321 INFO [stderr] 69 | | Dec 11 23:50:51.321 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 11 23:50:51.322 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 11 23:50:51.322 INFO [stderr] ... | Dec 11 23:50:51.322 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 11 23:50:51.323 INFO [stderr] 98 | | } Dec 11 23:50:51.323 INFO [stderr] | |_^ Dec 11 23:50:51.323 INFO [stderr] | Dec 11 23:50:51.323 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 11 23:50:51.324 INFO [stderr] Dec 11 23:50:51.324 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 11 23:50:51.324 INFO [stderr] --> src/main.rs:147:9 Dec 11 23:50:51.325 INFO [stderr] | Dec 11 23:50:51.325 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 11 23:50:51.325 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.325 INFO [stderr] Dec 11 23:50:51.326 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 11 23:50:51.326 INFO [stderr] --> src/main.rs:148:9 Dec 11 23:50:51.326 INFO [stderr] | Dec 11 23:50:51.326 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 11 23:50:51.326 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.326 INFO [stderr] Dec 11 23:50:51.327 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.328 INFO [stderr] --> src/main.rs:267:9 Dec 11 23:50:51.328 INFO [stderr] | Dec 11 23:50:51.328 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 11 23:50:51.328 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.328 INFO [stderr] | Dec 11 23:50:51.329 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 11 23:50:51.329 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.329 INFO [stderr] Dec 11 23:50:51.329 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.330 INFO [stderr] --> src/main.rs:269:9 Dec 11 23:50:51.330 INFO [stderr] | Dec 11 23:50:51.330 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 11 23:50:51.330 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.331 INFO [stderr] | Dec 11 23:50:51.331 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.331 INFO [stderr] Dec 11 23:50:51.331 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.332 INFO [stderr] --> src/main.rs:272:9 Dec 11 23:50:51.332 INFO [stderr] | Dec 11 23:50:51.332 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 11 23:50:51.332 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.332 INFO [stderr] | Dec 11 23:50:51.333 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.333 INFO [stderr] Dec 11 23:50:51.333 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.333 INFO [stderr] --> src/main.rs:274:5 Dec 11 23:50:51.334 INFO [stderr] | Dec 11 23:50:51.334 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 11 23:50:51.334 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.334 INFO [stderr] | Dec 11 23:50:51.335 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.335 INFO [stderr] Dec 11 23:50:51.335 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.335 INFO [stderr] --> src/main.rs:277:5 Dec 11 23:50:51.336 INFO [stderr] | Dec 11 23:50:51.336 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 11 23:50:51.336 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.336 INFO [stderr] | Dec 11 23:50:51.336 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.337 INFO [stderr] Dec 11 23:50:51.337 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.337 INFO [stderr] --> src/main.rs:280:5 Dec 11 23:50:51.337 INFO [stderr] | Dec 11 23:50:51.338 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 11 23:50:51.338 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.338 INFO [stderr] | Dec 11 23:50:51.338 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.339 INFO [stderr] Dec 11 23:50:51.339 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 11 23:50:51.339 INFO [stderr] --> src/main.rs:286:10 Dec 11 23:50:51.339 INFO [stderr] | Dec 11 23:50:51.340 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 11 23:50:51.340 INFO [stderr] | ^^^^^^^^^^^^ Dec 11 23:50:51.340 INFO [stderr] Dec 11 23:50:51.340 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 11 23:50:51.341 INFO [stderr] --> src/main.rs:357:9 Dec 11 23:50:51.341 INFO [stderr] | Dec 11 23:50:51.341 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 11 23:50:51.341 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.342 INFO [stderr] Dec 11 23:50:51.342 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 11 23:50:51.342 INFO [stderr] --> src/main.rs:387:17 Dec 11 23:50:51.343 INFO [stderr] | Dec 11 23:50:51.343 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 11 23:50:51.343 INFO [stderr] | ^^^^^^^^^^^^ Dec 11 23:50:51.343 INFO [stderr] Dec 11 23:50:51.470 INFO [stderr] warning: unused import: `std::io::prelude` Dec 11 23:50:51.471 INFO [stderr] --> src/main.rs:22:5 Dec 11 23:50:51.471 INFO [stderr] | Dec 11 23:50:51.471 INFO [stderr] 22 | use std::io::prelude::*; Dec 11 23:50:51.471 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 11 23:50:51.471 INFO [stderr] Dec 11 23:50:51.489 INFO [stderr] warning: unused variable: `consensus_base` Dec 11 23:50:51.489 INFO [stderr] --> src/main.rs:139:9 Dec 11 23:50:51.490 INFO [stderr] | Dec 11 23:50:51.490 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 11 23:50:51.490 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 11 23:50:51.490 INFO [stderr] | Dec 11 23:50:51.491 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 11 23:50:51.491 INFO [stderr] Dec 11 23:50:51.491 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 11 23:50:51.491 INFO [stderr] --> src/main.rs:144:13 Dec 11 23:50:51.491 INFO [stderr] | Dec 11 23:50:51.492 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 11 23:50:51.492 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 11 23:50:51.492 INFO [stderr] Dec 11 23:50:51.492 INFO [stderr] warning: unused variable: `chrom` Dec 11 23:50:51.492 INFO [stderr] --> src/main.rs:283:121 Dec 11 23:50:51.493 INFO [stderr] | Dec 11 23:50:51.493 INFO [stderr] 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) { Dec 11 23:50:51.493 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 11 23:50:51.493 INFO [stderr] Dec 11 23:50:51.493 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 11 23:50:51.494 INFO [stderr] --> src/main.rs:370:21 Dec 11 23:50:51.494 INFO [stderr] | Dec 11 23:50:51.494 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 11 23:50:51.494 INFO [stderr] | ^^^^^^^^^ Dec 11 23:50:51.494 INFO [stderr] | Dec 11 23:50:51.495 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 11 23:50:51.495 INFO [stderr] Dec 11 23:50:51.510 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.510 INFO [stderr] --> src/main.rs:74:9 Dec 11 23:50:51.511 INFO [stderr] | Dec 11 23:50:51.511 INFO [stderr] 74 | let mut pair; Dec 11 23:50:51.511 INFO [stderr] | ----^^^^ Dec 11 23:50:51.511 INFO [stderr] | | Dec 11 23:50:51.511 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.512 INFO [stderr] | Dec 11 23:50:51.512 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 11 23:50:51.512 INFO [stderr] Dec 11 23:50:51.512 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.512 INFO [stderr] --> src/main.rs:75:9 Dec 11 23:50:51.513 INFO [stderr] | Dec 11 23:50:51.513 INFO [stderr] 75 | let mut strand; Dec 11 23:50:51.513 INFO [stderr] | ----^^^^^^ Dec 11 23:50:51.513 INFO [stderr] | | Dec 11 23:50:51.514 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.514 INFO [stderr] Dec 11 23:50:51.514 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.514 INFO [stderr] --> src/main.rs:76:9 Dec 11 23:50:51.515 INFO [stderr] | Dec 11 23:50:51.515 INFO [stderr] 76 | let mut aln_pos; Dec 11 23:50:51.515 INFO [stderr] | ----^^^^^^^ Dec 11 23:50:51.515 INFO [stderr] | | Dec 11 23:50:51.516 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.516 INFO [stderr] Dec 11 23:50:51.552 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.552 INFO [stderr] --> src/main.rs:144:9 Dec 11 23:50:51.553 INFO [stderr] | Dec 11 23:50:51.553 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 11 23:50:51.553 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.553 INFO [stderr] | | Dec 11 23:50:51.554 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.554 INFO [stderr] Dec 11 23:50:51.554 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.554 INFO [stderr] --> src/main.rs:151:9 Dec 11 23:50:51.555 INFO [stderr] | Dec 11 23:50:51.555 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 11 23:50:51.555 INFO [stderr] | ----^^^^^^^^^ Dec 11 23:50:51.555 INFO [stderr] | | Dec 11 23:50:51.556 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.556 INFO [stderr] Dec 11 23:50:51.578 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.578 INFO [stderr] --> src/main.rs:338:9 Dec 11 23:50:51.578 INFO [stderr] | Dec 11 23:50:51.578 INFO [stderr] 338 | let mut need_trim:bool; Dec 11 23:50:51.578 INFO [stderr] | ----^^^^^^^^^ Dec 11 23:50:51.579 INFO [stderr] | | Dec 11 23:50:51.579 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.579 INFO [stderr] Dec 11 23:50:51.579 INFO [stderr] warning: variable does not need to be mutable Dec 11 23:50:51.579 INFO [stderr] --> src/main.rs:355:9 Dec 11 23:50:51.579 INFO [stderr] | Dec 11 23:50:51.579 INFO [stderr] 355 | let mut chrom = 0; Dec 11 23:50:51.580 INFO [stderr] | ----^^^^^ Dec 11 23:50:51.580 INFO [stderr] | | Dec 11 23:50:51.580 INFO [stderr] | help: remove this `mut` Dec 11 23:50:51.580 INFO [stderr] Dec 11 23:50:51.602 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 11 23:50:51.602 INFO [stderr] --> src/main.rs:68:1 Dec 11 23:50:51.602 INFO [stderr] | Dec 11 23:50:51.602 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 11 23:50:51.602 INFO [stderr] 69 | | Dec 11 23:50:51.602 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 11 23:50:51.602 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 11 23:50:51.602 INFO [stderr] ... | Dec 11 23:50:51.602 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 11 23:50:51.602 INFO [stderr] 98 | | } Dec 11 23:50:51.602 INFO [stderr] | |_^ Dec 11 23:50:51.602 INFO [stderr] | Dec 11 23:50:51.603 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 11 23:50:51.603 INFO [stderr] Dec 11 23:50:51.603 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 11 23:50:51.603 INFO [stderr] --> src/main.rs:147:9 Dec 11 23:50:51.603 INFO [stderr] | Dec 11 23:50:51.603 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 11 23:50:51.603 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.603 INFO [stderr] Dec 11 23:50:51.603 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 11 23:50:51.612 INFO [stderr] --> src/main.rs:148:9 Dec 11 23:50:51.612 INFO [stderr] | Dec 11 23:50:51.612 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 11 23:50:51.612 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.612 INFO [stderr] Dec 11 23:50:51.612 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.613 INFO [stderr] --> src/main.rs:267:9 Dec 11 23:50:51.613 INFO [stderr] | Dec 11 23:50:51.613 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 11 23:50:51.613 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.613 INFO [stderr] | Dec 11 23:50:51.613 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 11 23:50:51.613 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.613 INFO [stderr] Dec 11 23:50:51.613 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.614 INFO [stderr] --> src/main.rs:269:9 Dec 11 23:50:51.614 INFO [stderr] | Dec 11 23:50:51.614 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 11 23:50:51.614 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.615 INFO [stderr] | Dec 11 23:50:51.615 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.615 INFO [stderr] Dec 11 23:50:51.615 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.615 INFO [stderr] --> src/main.rs:272:9 Dec 11 23:50:51.616 INFO [stderr] | Dec 11 23:50:51.616 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 11 23:50:51.616 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.616 INFO [stderr] | Dec 11 23:50:51.617 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.617 INFO [stderr] Dec 11 23:50:51.617 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.617 INFO [stderr] --> src/main.rs:274:5 Dec 11 23:50:51.617 INFO [stderr] | Dec 11 23:50:51.618 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 11 23:50:51.618 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.618 INFO [stderr] | Dec 11 23:50:51.618 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.619 INFO [stderr] Dec 11 23:50:51.619 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.619 INFO [stderr] --> src/main.rs:277:5 Dec 11 23:50:51.619 INFO [stderr] | Dec 11 23:50:51.620 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 11 23:50:51.620 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.620 INFO [stderr] | Dec 11 23:50:51.620 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.620 INFO [stderr] Dec 11 23:50:51.621 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 11 23:50:51.621 INFO [stderr] --> src/main.rs:280:5 Dec 11 23:50:51.621 INFO [stderr] | Dec 11 23:50:51.621 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 11 23:50:51.622 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.622 INFO [stderr] | Dec 11 23:50:51.622 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 11 23:50:51.622 INFO [stderr] Dec 11 23:50:51.622 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 11 23:50:51.623 INFO [stderr] --> src/main.rs:286:10 Dec 11 23:50:51.623 INFO [stderr] | Dec 11 23:50:51.623 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 11 23:50:51.623 INFO [stderr] | ^^^^^^^^^^^^ Dec 11 23:50:51.623 INFO [stderr] Dec 11 23:50:51.624 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 11 23:50:51.624 INFO [stderr] --> src/main.rs:357:9 Dec 11 23:50:51.624 INFO [stderr] | Dec 11 23:50:51.624 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 11 23:50:51.624 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 11 23:50:51.624 INFO [stderr] Dec 11 23:50:51.624 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 11 23:50:51.624 INFO [stderr] --> src/main.rs:387:17 Dec 11 23:50:51.624 INFO [stderr] | Dec 11 23:50:51.624 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 11 23:50:51.624 INFO [stderr] | ^^^^^^^^^^^^ Dec 11 23:50:51.624 INFO [stderr] Dec 11 23:50:51.661 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 35.41s Dec 11 23:50:51.666 INFO [stderr] su: No module specific data is present Dec 11 23:50:53.341 INFO running `"docker" "inspect" "276a367bf9406fd63a0dd96728bfefefb6b61fe8bffdbb3373106728f0af6b45"` Dec 11 23:50:53.804 INFO running `"docker" "rm" "-f" "276a367bf9406fd63a0dd96728bfefefb6b61fe8bffdbb3373106728f0af6b45"` Dec 11 23:50:54.224 INFO [stdout] 276a367bf9406fd63a0dd96728bfefefb6b61fe8bffdbb3373106728f0af6b45