Dec 14 05:03:45.313 INFO testing TuBieJun/consensus against master#bd47d6825bf4090517549d33cfef10d3300b4a75 for pr-56550 Dec 14 05:03:45.313 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56550/worker-6/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-6/pr-56550/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/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 +bd47d6825bf4090517549d33cfef10d3300b4a75-alt build --frozen" "-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 14 05:03:45.851 INFO [stdout] 5c723766c60cb8535c5846e7520d51c382d55f5357f0a6a97d6b2ea85826991c Dec 14 05:03:45.853 INFO running `"docker" "start" "-a" "5c723766c60cb8535c5846e7520d51c382d55f5357f0a6a97d6b2ea85826991c"` Dec 14 05:03:48.435 INFO [stderr] usermod: no changes Dec 14 05:03:48.619 INFO [stderr] Compiling ieee754 v0.2.2 Dec 14 05:03:48.619 INFO [stderr] Compiling fs-utils v1.0.0 Dec 14 05:03:49.995 INFO [stderr] Compiling rust-htslib v0.15.0 Dec 14 05:04:21.612 INFO [stderr] Compiling consensus v0.1.0 (/source) Dec 14 05:04:23.047 INFO [stderr] warning: unused import: `std::env` Dec 14 05:04:23.047 INFO [stderr] --> src/main.rs:12:5 Dec 14 05:04:23.047 INFO [stderr] | Dec 14 05:04:23.047 INFO [stderr] 12 | use std::env; Dec 14 05:04:23.047 INFO [stderr] | ^^^^^^^^ Dec 14 05:04:23.047 INFO [stderr] | Dec 14 05:04:23.047 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 14 05:04:23.047 INFO [stderr] Dec 14 05:04:23.047 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 14 05:04:23.047 INFO [stderr] --> src/main.rs:16:5 Dec 14 05:04:23.047 INFO [stderr] | Dec 14 05:04:23.047 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 14 05:04:23.047 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.047 INFO [stderr] Dec 14 05:04:23.047 INFO [stderr] warning: unused import: `std::io` Dec 14 05:04:23.047 INFO [stderr] --> src/main.rs:21:5 Dec 14 05:04:23.047 INFO [stderr] | Dec 14 05:04:23.047 INFO [stderr] 21 | use std::io; Dec 14 05:04:23.047 INFO [stderr] | ^^^^^^^ Dec 14 05:04:23.047 INFO [stderr] Dec 14 05:04:23.047 INFO [stderr] warning: unused import: `PathBuf` Dec 14 05:04:23.047 INFO [stderr] --> src/main.rs:25:23 Dec 14 05:04:23.047 INFO [stderr] | Dec 14 05:04:23.047 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 14 05:04:23.047 INFO [stderr] | ^^^^^^^ Dec 14 05:04:23.047 INFO [stderr] Dec 14 05:04:23.047 INFO [stderr] warning: unused import: `SubCommand` Dec 14 05:04:23.047 INFO [stderr] --> src/main.rs:26:22 Dec 14 05:04:23.047 INFO [stderr] | Dec 14 05:04:23.047 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 14 05:04:23.047 INFO [stderr] | ^^^^^^^^^^ Dec 14 05:04:23.047 INFO [stderr] Dec 14 05:04:23.047 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 14 05:04:23.047 INFO [stderr] --> src/main.rs:218:20 Dec 14 05:04:23.047 INFO [stderr] | Dec 14 05:04:23.047 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 14 05:04:23.047 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 14 05:04:23.047 INFO [stderr] | Dec 14 05:04:23.047 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 14 05:04:23.047 INFO [stderr] Dec 14 05:04:23.047 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 14 05:04:23.047 INFO [stderr] --> src/main.rs:239:16 Dec 14 05:04:23.047 INFO [stderr] | Dec 14 05:04:23.047 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 14 05:04:23.047 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 14 05:04:23.047 INFO [stderr] Dec 14 05:04:23.191 INFO [stderr] warning: unused import: `std::io::prelude` Dec 14 05:04:23.191 INFO [stderr] --> src/main.rs:22:5 Dec 14 05:04:23.191 INFO [stderr] | Dec 14 05:04:23.191 INFO [stderr] 22 | use std::io::prelude::*; Dec 14 05:04:23.191 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 14 05:04:23.191 INFO [stderr] Dec 14 05:04:23.203 INFO [stderr] warning: unused variable: `consensus_base` Dec 14 05:04:23.203 INFO [stderr] --> src/main.rs:139:9 Dec 14 05:04:23.203 INFO [stderr] | Dec 14 05:04:23.203 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 14 05:04:23.203 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 14 05:04:23.203 INFO [stderr] | Dec 14 05:04:23.203 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 14 05:04:23.203 INFO [stderr] Dec 14 05:04:23.203 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 14 05:04:23.203 INFO [stderr] --> src/main.rs:144:13 Dec 14 05:04:23.203 INFO [stderr] | Dec 14 05:04:23.203 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 14 05:04:23.203 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 14 05:04:23.203 INFO [stderr] Dec 14 05:04:23.203 INFO [stderr] warning: unused variable: `chrom` Dec 14 05:04:23.203 INFO [stderr] --> src/main.rs:283:121 Dec 14 05:04:23.203 INFO [stderr] | Dec 14 05:04:23.203 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 14 05:04:23.203 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 14 05:04:23.203 INFO [stderr] Dec 14 05:04:23.203 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 14 05:04:23.203 INFO [stderr] --> src/main.rs:370:21 Dec 14 05:04:23.203 INFO [stderr] | Dec 14 05:04:23.203 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 14 05:04:23.203 INFO [stderr] | ^^^^^^^^^ Dec 14 05:04:23.203 INFO [stderr] | Dec 14 05:04:23.203 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 14 05:04:23.203 INFO [stderr] Dec 14 05:04:23.211 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:23.211 INFO [stderr] --> src/main.rs:74:9 Dec 14 05:04:23.211 INFO [stderr] | Dec 14 05:04:23.211 INFO [stderr] 74 | let mut pair; Dec 14 05:04:23.211 INFO [stderr] | ----^^^^ Dec 14 05:04:23.211 INFO [stderr] | | Dec 14 05:04:23.211 INFO [stderr] | help: remove this `mut` Dec 14 05:04:23.211 INFO [stderr] | Dec 14 05:04:23.211 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 14 05:04:23.211 INFO [stderr] Dec 14 05:04:23.211 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:23.211 INFO [stderr] --> src/main.rs:75:9 Dec 14 05:04:23.211 INFO [stderr] | Dec 14 05:04:23.211 INFO [stderr] 75 | let mut strand; Dec 14 05:04:23.211 INFO [stderr] | ----^^^^^^ Dec 14 05:04:23.211 INFO [stderr] | | Dec 14 05:04:23.211 INFO [stderr] | help: remove this `mut` Dec 14 05:04:23.211 INFO [stderr] Dec 14 05:04:23.211 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:23.211 INFO [stderr] --> src/main.rs:76:9 Dec 14 05:04:23.211 INFO [stderr] | Dec 14 05:04:23.211 INFO [stderr] 76 | let mut aln_pos; Dec 14 05:04:23.211 INFO [stderr] | ----^^^^^^^ Dec 14 05:04:23.211 INFO [stderr] | | Dec 14 05:04:23.211 INFO [stderr] | help: remove this `mut` Dec 14 05:04:23.211 INFO [stderr] Dec 14 05:04:23.239 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:23.239 INFO [stderr] --> src/main.rs:144:9 Dec 14 05:04:23.239 INFO [stderr] | Dec 14 05:04:23.239 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 14 05:04:23.239 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.239 INFO [stderr] | | Dec 14 05:04:23.239 INFO [stderr] | help: remove this `mut` Dec 14 05:04:23.239 INFO [stderr] Dec 14 05:04:23.239 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:23.239 INFO [stderr] --> src/main.rs:151:9 Dec 14 05:04:23.239 INFO [stderr] | Dec 14 05:04:23.239 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 14 05:04:23.239 INFO [stderr] | ----^^^^^^^^^ Dec 14 05:04:23.239 INFO [stderr] | | Dec 14 05:04:23.239 INFO [stderr] | help: remove this `mut` Dec 14 05:04:23.239 INFO [stderr] Dec 14 05:04:23.251 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:23.251 INFO [stderr] --> src/main.rs:338:9 Dec 14 05:04:23.251 INFO [stderr] | Dec 14 05:04:23.251 INFO [stderr] 338 | let mut need_trim:bool; Dec 14 05:04:23.251 INFO [stderr] | ----^^^^^^^^^ Dec 14 05:04:23.251 INFO [stderr] | | Dec 14 05:04:23.251 INFO [stderr] | help: remove this `mut` Dec 14 05:04:23.251 INFO [stderr] Dec 14 05:04:23.251 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:23.251 INFO [stderr] --> src/main.rs:355:9 Dec 14 05:04:23.251 INFO [stderr] | Dec 14 05:04:23.251 INFO [stderr] 355 | let mut chrom = 0; Dec 14 05:04:23.251 INFO [stderr] | ----^^^^^ Dec 14 05:04:23.251 INFO [stderr] | | Dec 14 05:04:23.251 INFO [stderr] | help: remove this `mut` Dec 14 05:04:23.251 INFO [stderr] Dec 14 05:04:23.263 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 14 05:04:23.263 INFO [stderr] --> src/main.rs:68:1 Dec 14 05:04:23.263 INFO [stderr] | Dec 14 05:04:23.263 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 14 05:04:23.263 INFO [stderr] 69 | | Dec 14 05:04:23.263 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 14 05:04:23.263 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 14 05:04:23.263 INFO [stderr] ... | Dec 14 05:04:23.263 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 14 05:04:23.263 INFO [stderr] 98 | | } Dec 14 05:04:23.263 INFO [stderr] | |_^ Dec 14 05:04:23.263 INFO [stderr] | Dec 14 05:04:23.263 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 14 05:04:23.263 INFO [stderr] Dec 14 05:04:23.263 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 14 05:04:23.263 INFO [stderr] --> src/main.rs:147:9 Dec 14 05:04:23.263 INFO [stderr] | Dec 14 05:04:23.263 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 14 05:04:23.263 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.263 INFO [stderr] Dec 14 05:04:23.263 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 14 05:04:23.263 INFO [stderr] --> src/main.rs:148:9 Dec 14 05:04:23.263 INFO [stderr] | Dec 14 05:04:23.263 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 14 05:04:23.263 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.263 INFO [stderr] Dec 14 05:04:23.263 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:23.263 INFO [stderr] --> src/main.rs:267:9 Dec 14 05:04:23.263 INFO [stderr] | Dec 14 05:04:23.263 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 14 05:04:23.263 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.263 INFO [stderr] | Dec 14 05:04:23.263 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 14 05:04:23.263 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:23.263 INFO [stderr] Dec 14 05:04:23.263 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:23.263 INFO [stderr] --> src/main.rs:269:9 Dec 14 05:04:23.263 INFO [stderr] | Dec 14 05:04:23.263 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 14 05:04:23.264 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:23.264 INFO [stderr] Dec 14 05:04:23.264 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:23.264 INFO [stderr] --> src/main.rs:272:9 Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 14 05:04:23.264 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:23.264 INFO [stderr] Dec 14 05:04:23.264 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:23.264 INFO [stderr] --> src/main.rs:274:5 Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 14 05:04:23.264 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:23.264 INFO [stderr] Dec 14 05:04:23.264 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:23.264 INFO [stderr] --> src/main.rs:277:5 Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 14 05:04:23.264 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:23.264 INFO [stderr] Dec 14 05:04:23.264 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:23.264 INFO [stderr] --> src/main.rs:280:5 Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 14 05:04:23.264 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:23.264 INFO [stderr] Dec 14 05:04:23.264 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 14 05:04:23.264 INFO [stderr] --> src/main.rs:286:10 Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 14 05:04:23.264 INFO [stderr] | ^^^^^^^^^^^^ Dec 14 05:04:23.264 INFO [stderr] Dec 14 05:04:23.264 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 14 05:04:23.264 INFO [stderr] --> src/main.rs:357:9 Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 14 05:04:23.264 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:23.264 INFO [stderr] Dec 14 05:04:23.264 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 14 05:04:23.264 INFO [stderr] --> src/main.rs:387:17 Dec 14 05:04:23.264 INFO [stderr] | Dec 14 05:04:23.264 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 14 05:04:23.264 INFO [stderr] | ^^^^^^^^^^^^ Dec 14 05:04:23.264 INFO [stderr] Dec 14 05:04:27.279 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 38.81s Dec 14 05:04:27.284 INFO [stderr] su: No module specific data is present Dec 14 05:04:28.115 INFO running `"docker" "inspect" "5c723766c60cb8535c5846e7520d51c382d55f5357f0a6a97d6b2ea85826991c"` Dec 14 05:04:28.500 INFO running `"docker" "rm" "-f" "5c723766c60cb8535c5846e7520d51c382d55f5357f0a6a97d6b2ea85826991c"` Dec 14 05:04:28.807 INFO [stdout] 5c723766c60cb8535c5846e7520d51c382d55f5357f0a6a97d6b2ea85826991c Dec 14 05:04:28.815 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56550/worker-6/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-6/pr-56550/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/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 +bd47d6825bf4090517549d33cfef10d3300b4a75-alt test --frozen --no-run" "-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 14 05:04:29.231 INFO [stdout] 88990367abbb5f61e8269c54b0ce2c09eaf1f3f2ef54becd6e094ce9071353ef Dec 14 05:04:29.235 INFO running `"docker" "start" "-a" "88990367abbb5f61e8269c54b0ce2c09eaf1f3f2ef54becd6e094ce9071353ef"` Dec 14 05:04:30.657 INFO [stderr] usermod: no changes Dec 14 05:04:30.783 INFO [stderr] Compiling consensus v0.1.0 (/source) Dec 14 05:04:32.347 INFO [stderr] warning: unused import: `std::env` Dec 14 05:04:32.347 INFO [stderr] --> src/main.rs:12:5 Dec 14 05:04:32.347 INFO [stderr] | Dec 14 05:04:32.347 INFO [stderr] 12 | use std::env; Dec 14 05:04:32.347 INFO [stderr] | ^^^^^^^^ Dec 14 05:04:32.347 INFO [stderr] | Dec 14 05:04:32.347 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 14 05:04:32.347 INFO [stderr] Dec 14 05:04:32.347 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 14 05:04:32.347 INFO [stderr] --> src/main.rs:16:5 Dec 14 05:04:32.347 INFO [stderr] | Dec 14 05:04:32.347 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 14 05:04:32.347 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.347 INFO [stderr] Dec 14 05:04:32.347 INFO [stderr] warning: unused import: `std::io` Dec 14 05:04:32.347 INFO [stderr] --> src/main.rs:21:5 Dec 14 05:04:32.347 INFO [stderr] | Dec 14 05:04:32.347 INFO [stderr] 21 | use std::io; Dec 14 05:04:32.347 INFO [stderr] | ^^^^^^^ Dec 14 05:04:32.347 INFO [stderr] Dec 14 05:04:32.347 INFO [stderr] warning: unused import: `PathBuf` Dec 14 05:04:32.347 INFO [stderr] --> src/main.rs:25:23 Dec 14 05:04:32.347 INFO [stderr] | Dec 14 05:04:32.347 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 14 05:04:32.347 INFO [stderr] | ^^^^^^^ Dec 14 05:04:32.347 INFO [stderr] Dec 14 05:04:32.347 INFO [stderr] warning: unused import: `SubCommand` Dec 14 05:04:32.347 INFO [stderr] --> src/main.rs:26:22 Dec 14 05:04:32.347 INFO [stderr] | Dec 14 05:04:32.347 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 14 05:04:32.347 INFO [stderr] | ^^^^^^^^^^ Dec 14 05:04:32.347 INFO [stderr] Dec 14 05:04:32.347 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 14 05:04:32.347 INFO [stderr] --> src/main.rs:218:20 Dec 14 05:04:32.347 INFO [stderr] | Dec 14 05:04:32.347 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 14 05:04:32.347 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 14 05:04:32.347 INFO [stderr] | Dec 14 05:04:32.347 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 14 05:04:32.347 INFO [stderr] Dec 14 05:04:32.347 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 14 05:04:32.347 INFO [stderr] --> src/main.rs:239:16 Dec 14 05:04:32.347 INFO [stderr] | Dec 14 05:04:32.347 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 14 05:04:32.347 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 14 05:04:32.347 INFO [stderr] Dec 14 05:04:32.509 INFO [stderr] warning: unused import: `std::io::prelude` Dec 14 05:04:32.509 INFO [stderr] --> src/main.rs:22:5 Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] 22 | use std::io::prelude::*; Dec 14 05:04:32.510 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 14 05:04:32.510 INFO [stderr] Dec 14 05:04:32.510 INFO [stderr] warning: unused variable: `consensus_base` Dec 14 05:04:32.510 INFO [stderr] --> src/main.rs:139:9 Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 14 05:04:32.510 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 14 05:04:32.510 INFO [stderr] Dec 14 05:04:32.510 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 14 05:04:32.510 INFO [stderr] --> src/main.rs:144:13 Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 14 05:04:32.510 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 14 05:04:32.510 INFO [stderr] Dec 14 05:04:32.510 INFO [stderr] warning: unused variable: `chrom` Dec 14 05:04:32.510 INFO [stderr] --> src/main.rs:283:121 Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 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 14 05:04:32.510 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 14 05:04:32.510 INFO [stderr] Dec 14 05:04:32.510 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 14 05:04:32.510 INFO [stderr] --> src/main.rs:370:21 Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 14 05:04:32.510 INFO [stderr] | ^^^^^^^^^ Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 14 05:04:32.510 INFO [stderr] Dec 14 05:04:32.510 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:32.510 INFO [stderr] --> src/main.rs:74:9 Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] 74 | let mut pair; Dec 14 05:04:32.510 INFO [stderr] | ----^^^^ Dec 14 05:04:32.510 INFO [stderr] | | Dec 14 05:04:32.510 INFO [stderr] | help: remove this `mut` Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 14 05:04:32.510 INFO [stderr] Dec 14 05:04:32.510 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:32.510 INFO [stderr] --> src/main.rs:75:9 Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] 75 | let mut strand; Dec 14 05:04:32.510 INFO [stderr] | ----^^^^^^ Dec 14 05:04:32.510 INFO [stderr] | | Dec 14 05:04:32.510 INFO [stderr] | help: remove this `mut` Dec 14 05:04:32.510 INFO [stderr] Dec 14 05:04:32.510 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:32.510 INFO [stderr] --> src/main.rs:76:9 Dec 14 05:04:32.510 INFO [stderr] | Dec 14 05:04:32.510 INFO [stderr] 76 | let mut aln_pos; Dec 14 05:04:32.510 INFO [stderr] | ----^^^^^^^ Dec 14 05:04:32.510 INFO [stderr] | | Dec 14 05:04:32.510 INFO [stderr] | help: remove this `mut` Dec 14 05:04:32.510 INFO [stderr] Dec 14 05:04:32.523 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:32.523 INFO [stderr] --> src/main.rs:144:9 Dec 14 05:04:32.523 INFO [stderr] | Dec 14 05:04:32.523 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 14 05:04:32.523 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.523 INFO [stderr] | | Dec 14 05:04:32.523 INFO [stderr] | help: remove this `mut` Dec 14 05:04:32.523 INFO [stderr] Dec 14 05:04:32.523 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:32.523 INFO [stderr] --> src/main.rs:151:9 Dec 14 05:04:32.523 INFO [stderr] | Dec 14 05:04:32.523 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 14 05:04:32.523 INFO [stderr] | ----^^^^^^^^^ Dec 14 05:04:32.523 INFO [stderr] | | Dec 14 05:04:32.523 INFO [stderr] | help: remove this `mut` Dec 14 05:04:32.523 INFO [stderr] Dec 14 05:04:32.541 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:32.541 INFO [stderr] --> src/main.rs:338:9 Dec 14 05:04:32.541 INFO [stderr] | Dec 14 05:04:32.541 INFO [stderr] 338 | let mut need_trim:bool; Dec 14 05:04:32.541 INFO [stderr] | ----^^^^^^^^^ Dec 14 05:04:32.541 INFO [stderr] | | Dec 14 05:04:32.541 INFO [stderr] | help: remove this `mut` Dec 14 05:04:32.541 INFO [stderr] Dec 14 05:04:32.541 INFO [stderr] warning: variable does not need to be mutable Dec 14 05:04:32.541 INFO [stderr] --> src/main.rs:355:9 Dec 14 05:04:32.541 INFO [stderr] | Dec 14 05:04:32.541 INFO [stderr] 355 | let mut chrom = 0; Dec 14 05:04:32.541 INFO [stderr] | ----^^^^^ Dec 14 05:04:32.541 INFO [stderr] | | Dec 14 05:04:32.541 INFO [stderr] | help: remove this `mut` Dec 14 05:04:32.541 INFO [stderr] Dec 14 05:04:32.602 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 14 05:04:32.602 INFO [stderr] --> src/main.rs:68:1 Dec 14 05:04:32.602 INFO [stderr] | Dec 14 05:04:32.602 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 14 05:04:32.602 INFO [stderr] 69 | | Dec 14 05:04:32.602 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 14 05:04:32.602 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 14 05:04:32.602 INFO [stderr] ... | Dec 14 05:04:32.602 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 14 05:04:32.602 INFO [stderr] 98 | | } Dec 14 05:04:32.602 INFO [stderr] | |_^ Dec 14 05:04:32.602 INFO [stderr] | Dec 14 05:04:32.602 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 14 05:04:32.602 INFO [stderr] Dec 14 05:04:32.602 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 14 05:04:32.602 INFO [stderr] --> src/main.rs:147:9 Dec 14 05:04:32.602 INFO [stderr] | Dec 14 05:04:32.602 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 14 05:04:32.602 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.602 INFO [stderr] Dec 14 05:04:32.602 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 14 05:04:32.602 INFO [stderr] --> src/main.rs:148:9 Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 14 05:04:32.603 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.603 INFO [stderr] Dec 14 05:04:32.603 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:32.603 INFO [stderr] --> src/main.rs:267:9 Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 14 05:04:32.603 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 14 05:04:32.603 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:32.603 INFO [stderr] Dec 14 05:04:32.603 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:32.603 INFO [stderr] --> src/main.rs:269:9 Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 14 05:04:32.603 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:32.603 INFO [stderr] Dec 14 05:04:32.603 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:32.603 INFO [stderr] --> src/main.rs:272:9 Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 14 05:04:32.603 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:32.603 INFO [stderr] Dec 14 05:04:32.603 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:32.603 INFO [stderr] --> src/main.rs:274:5 Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 14 05:04:32.603 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:32.603 INFO [stderr] Dec 14 05:04:32.603 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:32.603 INFO [stderr] --> src/main.rs:277:5 Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 14 05:04:32.603 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:32.603 INFO [stderr] Dec 14 05:04:32.603 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 14 05:04:32.603 INFO [stderr] --> src/main.rs:280:5 Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 14 05:04:32.603 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 14 05:04:32.603 INFO [stderr] Dec 14 05:04:32.603 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 14 05:04:32.603 INFO [stderr] --> src/main.rs:286:10 Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 14 05:04:32.603 INFO [stderr] | ^^^^^^^^^^^^ Dec 14 05:04:32.603 INFO [stderr] Dec 14 05:04:32.603 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 14 05:04:32.603 INFO [stderr] --> src/main.rs:357:9 Dec 14 05:04:32.603 INFO [stderr] | Dec 14 05:04:32.603 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 14 05:04:32.604 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 14 05:04:32.604 INFO [stderr] Dec 14 05:04:32.604 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 14 05:04:32.604 INFO [stderr] --> src/main.rs:387:17 Dec 14 05:04:32.604 INFO [stderr] | Dec 14 05:04:32.604 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 14 05:04:32.604 INFO [stderr] | ^^^^^^^^^^^^ Dec 14 05:04:32.604 INFO [stderr] Dec 14 05:04:33.007 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 2.31s Dec 14 05:04:33.008 INFO [stderr] su: No module specific data is present Dec 14 05:04:33.927 INFO running `"docker" "inspect" "88990367abbb5f61e8269c54b0ce2c09eaf1f3f2ef54becd6e094ce9071353ef"` Dec 14 05:04:34.287 INFO running `"docker" "rm" "-f" "88990367abbb5f61e8269c54b0ce2c09eaf1f3f2ef54becd6e094ce9071353ef"` Dec 14 05:04:34.619 INFO [stdout] 88990367abbb5f61e8269c54b0ce2c09eaf1f3f2ef54becd6e094ce9071353ef Dec 14 05:04:34.627 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56550/worker-6/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-6/pr-56550/master#bd47d6825bf4090517549d33cfef10d3300b4a75:/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 +bd47d6825bf4090517549d33cfef10d3300b4a75-alt test --frozen" "-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 14 05:04:35.139 INFO [stdout] 3fe8300313cbca608034c71f9470fd80b19c867523ce69bac535cc6b6965a3e9 Dec 14 05:04:35.144 INFO running `"docker" "start" "-a" "3fe8300313cbca608034c71f9470fd80b19c867523ce69bac535cc6b6965a3e9"` Dec 14 05:04:36.677 INFO [stderr] usermod: no changes Dec 14 05:04:36.763 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 0.07s Dec 14 05:04:36.775 INFO [stderr] Running /target/debug/deps/consensus-1cb56a748e2dea06 Dec 14 05:04:36.775 INFO [stdout] Dec 14 05:04:36.775 INFO [stdout] running 0 tests Dec 14 05:04:36.775 INFO [stdout] Dec 14 05:04:36.775 INFO [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 14 05:04:36.775 INFO [stdout] Dec 14 05:04:36.783 INFO [stderr] su: No module specific data is present Dec 14 05:04:38.635 INFO running `"docker" "inspect" "3fe8300313cbca608034c71f9470fd80b19c867523ce69bac535cc6b6965a3e9"` Dec 14 05:04:38.969 INFO running `"docker" "rm" "-f" "3fe8300313cbca608034c71f9470fd80b19c867523ce69bac535cc6b6965a3e9"` Dec 14 05:04:39.368 INFO [stdout] 3fe8300313cbca608034c71f9470fd80b19c867523ce69bac535cc6b6965a3e9