Dec 06 08:55:04.032 INFO testing TuBieJun/consensus against master#906deae0790bd18681b937fe9a141a3c26cf1855 for pr-56514 Dec 06 08:55:04.032 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-3/master#906deae0790bd18681b937fe9a141a3c26cf1855:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-3/pr-56514/master#906deae0790bd18681b937fe9a141a3c26cf1855:/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 +906deae0790bd18681b937fe9a141a3c26cf1855-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 06 08:55:04.476 INFO [stdout] 48db919f0cf06f1a8d9d245ae24dd02e7c35520fb3fa224b5e6865a531780b33 Dec 06 08:55:04.478 INFO running `"docker" "start" "-a" "48db919f0cf06f1a8d9d245ae24dd02e7c35520fb3fa224b5e6865a531780b33"` Dec 06 08:55:06.696 INFO [stderr] usermod: no changes Dec 06 08:55:06.825 INFO [stderr] Compiling ieee754 v0.2.2 Dec 06 08:55:06.832 INFO [stderr] Compiling fs-utils v1.0.0 Dec 06 08:55:07.821 INFO [stderr] Compiling rust-htslib v0.15.0 Dec 06 08:55:38.223 INFO [stderr] Compiling consensus v0.1.0 (/source) Dec 06 08:55:39.665 INFO [stderr] warning: unused import: `std::env` Dec 06 08:55:39.665 INFO [stderr] --> src/main.rs:12:5 Dec 06 08:55:39.665 INFO [stderr] | Dec 06 08:55:39.665 INFO [stderr] 12 | use std::env; Dec 06 08:55:39.665 INFO [stderr] | ^^^^^^^^ Dec 06 08:55:39.665 INFO [stderr] | Dec 06 08:55:39.665 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 06 08:55:39.665 INFO [stderr] Dec 06 08:55:39.665 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 06 08:55:39.665 INFO [stderr] --> src/main.rs:16:5 Dec 06 08:55:39.665 INFO [stderr] | Dec 06 08:55:39.665 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 06 08:55:39.665 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.665 INFO [stderr] Dec 06 08:55:39.665 INFO [stderr] warning: unused import: `std::io` Dec 06 08:55:39.665 INFO [stderr] --> src/main.rs:21:5 Dec 06 08:55:39.665 INFO [stderr] | Dec 06 08:55:39.665 INFO [stderr] 21 | use std::io; Dec 06 08:55:39.665 INFO [stderr] | ^^^^^^^ Dec 06 08:55:39.665 INFO [stderr] Dec 06 08:55:39.665 INFO [stderr] warning: unused import: `PathBuf` Dec 06 08:55:39.665 INFO [stderr] --> src/main.rs:25:23 Dec 06 08:55:39.665 INFO [stderr] | Dec 06 08:55:39.665 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 06 08:55:39.665 INFO [stderr] | ^^^^^^^ Dec 06 08:55:39.665 INFO [stderr] Dec 06 08:55:39.665 INFO [stderr] warning: unused import: `SubCommand` Dec 06 08:55:39.665 INFO [stderr] --> src/main.rs:26:22 Dec 06 08:55:39.665 INFO [stderr] | Dec 06 08:55:39.665 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 06 08:55:39.665 INFO [stderr] | ^^^^^^^^^^ Dec 06 08:55:39.665 INFO [stderr] Dec 06 08:55:39.665 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 06 08:55:39.665 INFO [stderr] --> src/main.rs:218:20 Dec 06 08:55:39.665 INFO [stderr] | Dec 06 08:55:39.665 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 06 08:55:39.665 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 06 08:55:39.665 INFO [stderr] | Dec 06 08:55:39.665 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 06 08:55:39.665 INFO [stderr] Dec 06 08:55:39.665 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 06 08:55:39.665 INFO [stderr] --> src/main.rs:239:16 Dec 06 08:55:39.665 INFO [stderr] | Dec 06 08:55:39.665 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 06 08:55:39.665 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 06 08:55:39.665 INFO [stderr] Dec 06 08:55:39.787 INFO [stderr] warning: unused import: `std::io::prelude` Dec 06 08:55:39.788 INFO [stderr] --> src/main.rs:22:5 Dec 06 08:55:39.788 INFO [stderr] | Dec 06 08:55:39.788 INFO [stderr] 22 | use std::io::prelude::*; Dec 06 08:55:39.789 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 06 08:55:39.789 INFO [stderr] Dec 06 08:55:39.797 INFO [stderr] warning: unused variable: `consensus_base` Dec 06 08:55:39.797 INFO [stderr] --> src/main.rs:139:9 Dec 06 08:55:39.798 INFO [stderr] | Dec 06 08:55:39.798 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 06 08:55:39.798 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 06 08:55:39.799 INFO [stderr] | Dec 06 08:55:39.799 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 06 08:55:39.799 INFO [stderr] Dec 06 08:55:39.799 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 06 08:55:39.800 INFO [stderr] --> src/main.rs:144:13 Dec 06 08:55:39.800 INFO [stderr] | Dec 06 08:55:39.800 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 06 08:55:39.801 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 06 08:55:39.801 INFO [stderr] Dec 06 08:55:39.801 INFO [stderr] warning: unused variable: `chrom` Dec 06 08:55:39.802 INFO [stderr] --> src/main.rs:283:121 Dec 06 08:55:39.802 INFO [stderr] | Dec 06 08:55:39.802 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 06 08:55:39.803 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 06 08:55:39.803 INFO [stderr] Dec 06 08:55:39.803 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 06 08:55:39.803 INFO [stderr] --> src/main.rs:370:21 Dec 06 08:55:39.804 INFO [stderr] | Dec 06 08:55:39.804 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 06 08:55:39.804 INFO [stderr] | ^^^^^^^^^ Dec 06 08:55:39.805 INFO [stderr] | Dec 06 08:55:39.805 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 06 08:55:39.805 INFO [stderr] Dec 06 08:55:39.806 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:39.806 INFO [stderr] --> src/main.rs:74:9 Dec 06 08:55:39.806 INFO [stderr] | Dec 06 08:55:39.807 INFO [stderr] 74 | let mut pair; Dec 06 08:55:39.807 INFO [stderr] | ----^^^^ Dec 06 08:55:39.807 INFO [stderr] | | Dec 06 08:55:39.808 INFO [stderr] | help: remove this `mut` Dec 06 08:55:39.808 INFO [stderr] | Dec 06 08:55:39.808 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 06 08:55:39.808 INFO [stderr] Dec 06 08:55:39.809 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:39.809 INFO [stderr] --> src/main.rs:75:9 Dec 06 08:55:39.809 INFO [stderr] | Dec 06 08:55:39.810 INFO [stderr] 75 | let mut strand; Dec 06 08:55:39.810 INFO [stderr] | ----^^^^^^ Dec 06 08:55:39.810 INFO [stderr] | | Dec 06 08:55:39.810 INFO [stderr] | help: remove this `mut` Dec 06 08:55:39.811 INFO [stderr] Dec 06 08:55:39.811 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:39.811 INFO [stderr] --> src/main.rs:76:9 Dec 06 08:55:39.811 INFO [stderr] | Dec 06 08:55:39.811 INFO [stderr] 76 | let mut aln_pos; Dec 06 08:55:39.811 INFO [stderr] | ----^^^^^^^ Dec 06 08:55:39.811 INFO [stderr] | | Dec 06 08:55:39.811 INFO [stderr] | help: remove this `mut` Dec 06 08:55:39.812 INFO [stderr] Dec 06 08:55:39.834 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:39.834 INFO [stderr] --> src/main.rs:144:9 Dec 06 08:55:39.834 INFO [stderr] | Dec 06 08:55:39.835 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 06 08:55:39.835 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.835 INFO [stderr] | | Dec 06 08:55:39.836 INFO [stderr] | help: remove this `mut` Dec 06 08:55:39.836 INFO [stderr] Dec 06 08:55:39.836 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:39.836 INFO [stderr] --> src/main.rs:151:9 Dec 06 08:55:39.837 INFO [stderr] | Dec 06 08:55:39.837 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 06 08:55:39.837 INFO [stderr] | ----^^^^^^^^^ Dec 06 08:55:39.838 INFO [stderr] | | Dec 06 08:55:39.838 INFO [stderr] | help: remove this `mut` Dec 06 08:55:39.838 INFO [stderr] Dec 06 08:55:39.847 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:39.847 INFO [stderr] --> src/main.rs:338:9 Dec 06 08:55:39.848 INFO [stderr] | Dec 06 08:55:39.848 INFO [stderr] 338 | let mut need_trim:bool; Dec 06 08:55:39.848 INFO [stderr] | ----^^^^^^^^^ Dec 06 08:55:39.849 INFO [stderr] | | Dec 06 08:55:39.849 INFO [stderr] | help: remove this `mut` Dec 06 08:55:39.849 INFO [stderr] Dec 06 08:55:39.849 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:39.850 INFO [stderr] --> src/main.rs:355:9 Dec 06 08:55:39.850 INFO [stderr] | Dec 06 08:55:39.850 INFO [stderr] 355 | let mut chrom = 0; Dec 06 08:55:39.851 INFO [stderr] | ----^^^^^ Dec 06 08:55:39.851 INFO [stderr] | | Dec 06 08:55:39.851 INFO [stderr] | help: remove this `mut` Dec 06 08:55:39.851 INFO [stderr] Dec 06 08:55:39.859 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 06 08:55:39.859 INFO [stderr] --> src/main.rs:68:1 Dec 06 08:55:39.859 INFO [stderr] | Dec 06 08:55:39.860 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 06 08:55:39.860 INFO [stderr] 69 | | Dec 06 08:55:39.860 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 06 08:55:39.861 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 06 08:55:39.861 INFO [stderr] ... | Dec 06 08:55:39.861 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 06 08:55:39.862 INFO [stderr] 98 | | } Dec 06 08:55:39.862 INFO [stderr] | |_^ Dec 06 08:55:39.862 INFO [stderr] | Dec 06 08:55:39.862 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 06 08:55:39.863 INFO [stderr] Dec 06 08:55:39.863 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 06 08:55:39.863 INFO [stderr] --> src/main.rs:147:9 Dec 06 08:55:39.864 INFO [stderr] | Dec 06 08:55:39.864 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 06 08:55:39.864 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.864 INFO [stderr] Dec 06 08:55:39.865 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 06 08:55:39.865 INFO [stderr] --> src/main.rs:148:9 Dec 06 08:55:39.865 INFO [stderr] | Dec 06 08:55:39.866 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 06 08:55:39.866 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.866 INFO [stderr] Dec 06 08:55:39.866 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:39.867 INFO [stderr] --> src/main.rs:267:9 Dec 06 08:55:39.867 INFO [stderr] | Dec 06 08:55:39.867 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 06 08:55:39.868 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.868 INFO [stderr] | Dec 06 08:55:39.868 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 06 08:55:39.869 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:39.869 INFO [stderr] Dec 06 08:55:39.869 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:39.869 INFO [stderr] --> src/main.rs:269:9 Dec 06 08:55:39.870 INFO [stderr] | Dec 06 08:55:39.870 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 06 08:55:39.870 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.871 INFO [stderr] | Dec 06 08:55:39.871 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:39.871 INFO [stderr] Dec 06 08:55:39.872 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:39.872 INFO [stderr] --> src/main.rs:272:9 Dec 06 08:55:39.872 INFO [stderr] | Dec 06 08:55:39.873 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 06 08:55:39.873 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.873 INFO [stderr] | Dec 06 08:55:39.874 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:39.874 INFO [stderr] Dec 06 08:55:39.874 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:39.875 INFO [stderr] --> src/main.rs:274:5 Dec 06 08:55:39.875 INFO [stderr] | Dec 06 08:55:39.875 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 06 08:55:39.876 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.876 INFO [stderr] | Dec 06 08:55:39.876 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:39.876 INFO [stderr] Dec 06 08:55:39.877 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:39.877 INFO [stderr] --> src/main.rs:277:5 Dec 06 08:55:39.877 INFO [stderr] | Dec 06 08:55:39.877 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 06 08:55:39.878 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.878 INFO [stderr] | Dec 06 08:55:39.878 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:39.878 INFO [stderr] Dec 06 08:55:39.879 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:39.879 INFO [stderr] --> src/main.rs:280:5 Dec 06 08:55:39.879 INFO [stderr] | Dec 06 08:55:39.879 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 06 08:55:39.880 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.880 INFO [stderr] | Dec 06 08:55:39.880 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:39.880 INFO [stderr] Dec 06 08:55:39.881 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 06 08:55:39.881 INFO [stderr] --> src/main.rs:286:10 Dec 06 08:55:39.881 INFO [stderr] | Dec 06 08:55:39.881 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 06 08:55:39.882 INFO [stderr] | ^^^^^^^^^^^^ Dec 06 08:55:39.882 INFO [stderr] Dec 06 08:55:39.882 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 06 08:55:39.882 INFO [stderr] --> src/main.rs:357:9 Dec 06 08:55:39.883 INFO [stderr] | Dec 06 08:55:39.883 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 06 08:55:39.883 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:39.883 INFO [stderr] Dec 06 08:55:39.884 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 06 08:55:39.884 INFO [stderr] --> src/main.rs:387:17 Dec 06 08:55:39.884 INFO [stderr] | Dec 06 08:55:39.885 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 06 08:55:39.885 INFO [stderr] | ^^^^^^^^^^^^ Dec 06 08:55:39.885 INFO [stderr] Dec 06 08:55:43.808 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 37.09s Dec 06 08:55:43.814 INFO [stderr] su: No module specific data is present Dec 06 08:55:44.604 INFO running `"docker" "inspect" "48db919f0cf06f1a8d9d245ae24dd02e7c35520fb3fa224b5e6865a531780b33"` Dec 06 08:55:44.982 INFO running `"docker" "rm" "-f" "48db919f0cf06f1a8d9d245ae24dd02e7c35520fb3fa224b5e6865a531780b33"` Dec 06 08:55:45.324 INFO [stdout] 48db919f0cf06f1a8d9d245ae24dd02e7c35520fb3fa224b5e6865a531780b33 Dec 06 08:55:45.330 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-3/master#906deae0790bd18681b937fe9a141a3c26cf1855:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-3/pr-56514/master#906deae0790bd18681b937fe9a141a3c26cf1855:/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 +906deae0790bd18681b937fe9a141a3c26cf1855-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 06 08:55:45.842 INFO [stdout] 7d9791d5414dcf99defbec95b8b23b07dbc9c1e29f3901c34c99f5aa3b632563 Dec 06 08:55:45.844 INFO running `"docker" "start" "-a" "7d9791d5414dcf99defbec95b8b23b07dbc9c1e29f3901c34c99f5aa3b632563"` Dec 06 08:55:48.288 INFO [stderr] usermod: no changes Dec 06 08:55:48.396 INFO [stderr] Compiling consensus v0.1.0 (/source) Dec 06 08:55:49.812 INFO [stderr] warning: unused import: `std::env` Dec 06 08:55:49.812 INFO [stderr] --> src/main.rs:12:5 Dec 06 08:55:49.812 INFO [stderr] | Dec 06 08:55:49.812 INFO [stderr] 12 | use std::env; Dec 06 08:55:49.812 INFO [stderr] | ^^^^^^^^ Dec 06 08:55:49.812 INFO [stderr] | Dec 06 08:55:49.812 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 06 08:55:49.812 INFO [stderr] Dec 06 08:55:49.812 INFO [stderr] warning: unused import: `rust_htslib::prelude::*` Dec 06 08:55:49.812 INFO [stderr] --> src/main.rs:16:5 Dec 06 08:55:49.812 INFO [stderr] | Dec 06 08:55:49.812 INFO [stderr] 16 | use rust_htslib::prelude::*; Dec 06 08:55:49.812 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.812 INFO [stderr] Dec 06 08:55:49.812 INFO [stderr] warning: unused import: `std::io` Dec 06 08:55:49.812 INFO [stderr] --> src/main.rs:21:5 Dec 06 08:55:49.812 INFO [stderr] | Dec 06 08:55:49.813 INFO [stderr] 21 | use std::io; Dec 06 08:55:49.813 INFO [stderr] | ^^^^^^^ Dec 06 08:55:49.813 INFO [stderr] Dec 06 08:55:49.813 INFO [stderr] warning: unused import: `PathBuf` Dec 06 08:55:49.813 INFO [stderr] --> src/main.rs:25:23 Dec 06 08:55:49.813 INFO [stderr] | Dec 06 08:55:49.813 INFO [stderr] 25 | use std::path::{Path, PathBuf}; Dec 06 08:55:49.813 INFO [stderr] | ^^^^^^^ Dec 06 08:55:49.813 INFO [stderr] Dec 06 08:55:49.813 INFO [stderr] warning: unused import: `SubCommand` Dec 06 08:55:49.813 INFO [stderr] --> src/main.rs:26:22 Dec 06 08:55:49.813 INFO [stderr] | Dec 06 08:55:49.813 INFO [stderr] 26 | use clap::{Arg, App, SubCommand}; Dec 06 08:55:49.813 INFO [stderr] | ^^^^^^^^^^ Dec 06 08:55:49.813 INFO [stderr] Dec 06 08:55:49.813 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 06 08:55:49.813 INFO [stderr] --> src/main.rs:218:20 Dec 06 08:55:49.813 INFO [stderr] | Dec 06 08:55:49.813 INFO [stderr] 218 | if (num_position[&(i as usize)] == num_position[&(0 as usize)]) { Dec 06 08:55:49.813 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 06 08:55:49.813 INFO [stderr] | Dec 06 08:55:49.813 INFO [stderr] = note: #[warn(unused_parens)] on by default Dec 06 08:55:49.813 INFO [stderr] Dec 06 08:55:49.813 INFO [stderr] warning: unnecessary parentheses around `if` condition Dec 06 08:55:49.813 INFO [stderr] --> src/main.rs:239:16 Dec 06 08:55:49.813 INFO [stderr] | Dec 06 08:55:49.813 INFO [stderr] 239 | if (baseEach_percent_record.len() > 0) { Dec 06 08:55:49.813 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove these parentheses Dec 06 08:55:49.813 INFO [stderr] Dec 06 08:55:49.924 INFO [stderr] warning: unused import: `std::io::prelude` Dec 06 08:55:49.924 INFO [stderr] --> src/main.rs:22:5 Dec 06 08:55:49.924 INFO [stderr] | Dec 06 08:55:49.924 INFO [stderr] 22 | use std::io::prelude::*; Dec 06 08:55:49.924 INFO [stderr] | ^^^^^^^^^^^^^^^^ Dec 06 08:55:49.924 INFO [stderr] Dec 06 08:55:49.936 INFO [stderr] warning: unused variable: `consensus_base` Dec 06 08:55:49.936 INFO [stderr] --> src/main.rs:139:9 Dec 06 08:55:49.936 INFO [stderr] | Dec 06 08:55:49.936 INFO [stderr] 139 | let consensus_base:Vec = Vec::new(); Dec 06 08:55:49.936 INFO [stderr] | ^^^^^^^^^^^^^^ help: consider using `_consensus_base` instead Dec 06 08:55:49.936 INFO [stderr] | Dec 06 08:55:49.936 INFO [stderr] = note: #[warn(unused_variables)] on by default Dec 06 08:55:49.936 INFO [stderr] Dec 06 08:55:49.936 INFO [stderr] warning: unused variable: `consensus_source_reads` Dec 06 08:55:49.936 INFO [stderr] --> src/main.rs:144:13 Dec 06 08:55:49.936 INFO [stderr] | Dec 06 08:55:49.936 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 06 08:55:49.936 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ help: consider using `_consensus_source_reads` instead Dec 06 08:55:49.936 INFO [stderr] Dec 06 08:55:49.936 INFO [stderr] warning: unused variable: `chrom` Dec 06 08:55:49.936 INFO [stderr] --> src/main.rs:283:121 Dec 06 08:55:49.936 INFO [stderr] | Dec 06 08:55:49.937 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 06 08:55:49.937 INFO [stderr] | ^^^^^ help: consider using `_chrom` instead Dec 06 08:55:49.937 INFO [stderr] Dec 06 08:55:49.937 INFO [stderr] warning: value assigned to `new_seq_b` is never read Dec 06 08:55:49.937 INFO [stderr] --> src/main.rs:370:21 Dec 06 08:55:49.937 INFO [stderr] | Dec 06 08:55:49.937 INFO [stderr] 370 | let mut new_seq_b:Vec = Vec::new(); Dec 06 08:55:49.937 INFO [stderr] | ^^^^^^^^^ Dec 06 08:55:49.937 INFO [stderr] | Dec 06 08:55:49.937 INFO [stderr] = note: #[warn(unused_assignments)] on by default Dec 06 08:55:49.937 INFO [stderr] Dec 06 08:55:49.944 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:49.944 INFO [stderr] --> src/main.rs:74:9 Dec 06 08:55:49.944 INFO [stderr] | Dec 06 08:55:49.944 INFO [stderr] 74 | let mut pair; Dec 06 08:55:49.944 INFO [stderr] | ----^^^^ Dec 06 08:55:49.944 INFO [stderr] | | Dec 06 08:55:49.944 INFO [stderr] | help: remove this `mut` Dec 06 08:55:49.944 INFO [stderr] | Dec 06 08:55:49.944 INFO [stderr] = note: #[warn(unused_mut)] on by default Dec 06 08:55:49.944 INFO [stderr] Dec 06 08:55:49.944 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:49.944 INFO [stderr] --> src/main.rs:75:9 Dec 06 08:55:49.944 INFO [stderr] | Dec 06 08:55:49.944 INFO [stderr] 75 | let mut strand; Dec 06 08:55:49.944 INFO [stderr] | ----^^^^^^ Dec 06 08:55:49.944 INFO [stderr] | | Dec 06 08:55:49.944 INFO [stderr] | help: remove this `mut` Dec 06 08:55:49.944 INFO [stderr] Dec 06 08:55:49.944 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:49.944 INFO [stderr] --> src/main.rs:76:9 Dec 06 08:55:49.944 INFO [stderr] | Dec 06 08:55:49.945 INFO [stderr] 76 | let mut aln_pos; Dec 06 08:55:49.945 INFO [stderr] | ----^^^^^^^ Dec 06 08:55:49.945 INFO [stderr] | | Dec 06 08:55:49.945 INFO [stderr] | help: remove this `mut` Dec 06 08:55:49.945 INFO [stderr] Dec 06 08:55:49.971 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:49.971 INFO [stderr] --> src/main.rs:144:9 Dec 06 08:55:49.971 INFO [stderr] | Dec 06 08:55:49.971 INFO [stderr] 144 | let mut consensus_source_reads = String::new(); Dec 06 08:55:49.971 INFO [stderr] | ----^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.971 INFO [stderr] | | Dec 06 08:55:49.971 INFO [stderr] | help: remove this `mut` Dec 06 08:55:49.971 INFO [stderr] Dec 06 08:55:49.971 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:49.971 INFO [stderr] --> src/main.rs:151:9 Dec 06 08:55:49.971 INFO [stderr] | Dec 06 08:55:49.971 INFO [stderr] 151 | let mut top_cigar:&CigarStringView; Dec 06 08:55:49.971 INFO [stderr] | ----^^^^^^^^^ Dec 06 08:55:49.971 INFO [stderr] | | Dec 06 08:55:49.971 INFO [stderr] | help: remove this `mut` Dec 06 08:55:49.971 INFO [stderr] Dec 06 08:55:49.984 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:49.984 INFO [stderr] --> src/main.rs:338:9 Dec 06 08:55:49.984 INFO [stderr] | Dec 06 08:55:49.984 INFO [stderr] 338 | let mut need_trim:bool; Dec 06 08:55:49.984 INFO [stderr] | ----^^^^^^^^^ Dec 06 08:55:49.984 INFO [stderr] | | Dec 06 08:55:49.984 INFO [stderr] | help: remove this `mut` Dec 06 08:55:49.984 INFO [stderr] Dec 06 08:55:49.984 INFO [stderr] warning: variable does not need to be mutable Dec 06 08:55:49.984 INFO [stderr] --> src/main.rs:355:9 Dec 06 08:55:49.984 INFO [stderr] | Dec 06 08:55:49.984 INFO [stderr] 355 | let mut chrom = 0; Dec 06 08:55:49.984 INFO [stderr] | ----^^^^^ Dec 06 08:55:49.984 INFO [stderr] | | Dec 06 08:55:49.984 INFO [stderr] | help: remove this `mut` Dec 06 08:55:49.984 INFO [stderr] Dec 06 08:55:49.996 INFO [stderr] warning: function `bamLineParse` should have a snake case name such as `bam_line_parse` Dec 06 08:55:49.996 INFO [stderr] --> src/main.rs:68:1 Dec 06 08:55:49.996 INFO [stderr] | Dec 06 08:55:49.996 INFO [stderr] 68 | / fn bamLineParse(record:&Record) -> (String, String, String, i32, i32){ Dec 06 08:55:49.996 INFO [stderr] 69 | | Dec 06 08:55:49.996 INFO [stderr] 70 | | let qname_str = String::from_utf8_lossy(record.qname()).to_string(); Dec 06 08:55:49.996 INFO [stderr] 71 | | let temp_v:Vec<&str> = qname_str.split('#').collect(); Dec 06 08:55:49.996 INFO [stderr] ... | Dec 06 08:55:49.996 INFO [stderr] 97 | | (index, pair.to_string(), strand.to_string(), insert_size.abs(), aln_pos) Dec 06 08:55:49.996 INFO [stderr] 98 | | } Dec 06 08:55:49.996 INFO [stderr] | |_^ Dec 06 08:55:49.996 INFO [stderr] | Dec 06 08:55:49.996 INFO [stderr] = note: #[warn(non_snake_case)] on by default Dec 06 08:55:49.996 INFO [stderr] Dec 06 08:55:49.996 INFO [stderr] warning: variable `baseEach_num_record` should have a snake case name such as `base_each_num_record` Dec 06 08:55:49.996 INFO [stderr] --> src/main.rs:147:9 Dec 06 08:55:49.996 INFO [stderr] | Dec 06 08:55:49.996 INFO [stderr] 147 | let mut baseEach_num_record = String::new(); Dec 06 08:55:49.996 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.997 INFO [stderr] Dec 06 08:55:49.997 INFO [stderr] warning: variable `baseEach_percent_record` should have a snake case name such as `base_each_percent_record` Dec 06 08:55:49.997 INFO [stderr] --> src/main.rs:148:9 Dec 06 08:55:49.997 INFO [stderr] | Dec 06 08:55:49.997 INFO [stderr] 148 | let mut baseEach_percent_record = String::new(); Dec 06 08:55:49.997 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.997 INFO [stderr] Dec 06 08:55:49.997 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:49.997 INFO [stderr] --> src/main.rs:267:9 Dec 06 08:55:49.997 INFO [stderr] | Dec 06 08:55:49.997 INFO [stderr] 267 | o_buff.write(&member_record.2); Dec 06 08:55:49.997 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.997 INFO [stderr] | Dec 06 08:55:49.997 INFO [stderr] = note: #[warn(unused_must_use)] on by default Dec 06 08:55:49.997 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:49.997 INFO [stderr] Dec 06 08:55:49.997 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:49.997 INFO [stderr] --> src/main.rs:269:9 Dec 06 08:55:49.997 INFO [stderr] | Dec 06 08:55:49.997 INFO [stderr] 269 | o_buff.write(&member_record.0); Dec 06 08:55:49.997 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.997 INFO [stderr] | Dec 06 08:55:49.997 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:49.997 INFO [stderr] Dec 06 08:55:49.997 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:49.997 INFO [stderr] --> src/main.rs:272:9 Dec 06 08:55:49.997 INFO [stderr] | Dec 06 08:55:49.997 INFO [stderr] 272 | o_buff.write(&real_qual_temp); Dec 06 08:55:49.997 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.997 INFO [stderr] | Dec 06 08:55:49.997 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:49.997 INFO [stderr] Dec 06 08:55:49.997 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:49.997 INFO [stderr] --> src/main.rs:274:5 Dec 06 08:55:49.997 INFO [stderr] | Dec 06 08:55:49.997 INFO [stderr] 274 | o_buff.write(b"\n"); Dec 06 08:55:49.997 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.997 INFO [stderr] | Dec 06 08:55:49.997 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:49.997 INFO [stderr] Dec 06 08:55:49.997 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:49.998 INFO [stderr] --> src/main.rs:277:5 Dec 06 08:55:49.998 INFO [stderr] | Dec 06 08:55:49.998 INFO [stderr] 277 | o_buff.write(b"\n"); Dec 06 08:55:49.998 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.998 INFO [stderr] | Dec 06 08:55:49.998 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:49.998 INFO [stderr] Dec 06 08:55:49.998 INFO [stderr] warning: unused `std::result::Result` that must be used Dec 06 08:55:49.998 INFO [stderr] --> src/main.rs:280:5 Dec 06 08:55:49.998 INFO [stderr] | Dec 06 08:55:49.998 INFO [stderr] 280 | o_buff.write(b"\n"); Dec 06 08:55:49.998 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.998 INFO [stderr] | Dec 06 08:55:49.998 INFO [stderr] = note: this `Result` may be an `Err` variant, which should be handled Dec 06 08:55:49.998 INFO [stderr] Dec 06 08:55:49.998 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 06 08:55:49.998 INFO [stderr] --> src/main.rs:286:10 Dec 06 08:55:49.998 INFO [stderr] | Dec 06 08:55:49.998 INFO [stderr] 286 | for (key_dupGroup, pair_dup) in pd.iter() { Dec 06 08:55:49.998 INFO [stderr] | ^^^^^^^^^^^^ Dec 06 08:55:49.998 INFO [stderr] Dec 06 08:55:49.998 INFO [stderr] warning: variable `position_dupGroup` should have a snake case name such as `position_dup_group` Dec 06 08:55:49.998 INFO [stderr] --> src/main.rs:357:9 Dec 06 08:55:49.998 INFO [stderr] | Dec 06 08:55:49.998 INFO [stderr] 357 | let mut position_dupGroup: HashMap, Vec, Vec, CigarStringView, bool)>>> = HashMap::new(); Dec 06 08:55:49.998 INFO [stderr] | ^^^^^^^^^^^^^^^^^^^^^ Dec 06 08:55:49.998 INFO [stderr] Dec 06 08:55:49.998 INFO [stderr] warning: variable `key_dupGroup` should have a snake case name such as `key_dup_group` Dec 06 08:55:49.998 INFO [stderr] --> src/main.rs:387:17 Dec 06 08:55:49.998 INFO [stderr] | Dec 06 08:55:49.998 INFO [stderr] 387 | let key_dupGroup = format!("{}_{}_{}_{}{}", index, chrom, aln_pos, strand, insert_size); Dec 06 08:55:49.998 INFO [stderr] | ^^^^^^^^^^^^ Dec 06 08:55:49.998 INFO [stderr] Dec 06 08:55:50.439 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 2.13s Dec 06 08:55:50.445 INFO [stderr] su: No module specific data is present Dec 06 08:55:51.292 INFO running `"docker" "inspect" "7d9791d5414dcf99defbec95b8b23b07dbc9c1e29f3901c34c99f5aa3b632563"` Dec 06 08:55:51.614 INFO running `"docker" "rm" "-f" "7d9791d5414dcf99defbec95b8b23b07dbc9c1e29f3901c34c99f5aa3b632563"` Dec 06 08:55:51.964 INFO [stdout] 7d9791d5414dcf99defbec95b8b23b07dbc9c1e29f3901c34c99f5aa3b632563 Dec 06 08:55:51.970 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-3/master#906deae0790bd18681b937fe9a141a3c26cf1855:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-3/pr-56514/master#906deae0790bd18681b937fe9a141a3c26cf1855:/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 +906deae0790bd18681b937fe9a141a3c26cf1855-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 06 08:55:52.468 INFO [stdout] 13fb7bcbbb8e07f5677e7685afb16c1bb890607047a2aee1f0cf741d128d7e3f Dec 06 08:55:52.470 INFO running `"docker" "start" "-a" "13fb7bcbbb8e07f5677e7685afb16c1bb890607047a2aee1f0cf741d128d7e3f"` Dec 06 08:55:54.455 INFO [stderr] usermod: no changes Dec 06 08:55:54.588 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 0.10s Dec 06 08:55:54.588 INFO [stderr] Running /target/debug/deps/consensus-2eb782c6f820d69f Dec 06 08:55:54.600 INFO [stdout] Dec 06 08:55:54.600 INFO [stdout] running 0 tests Dec 06 08:55:54.600 INFO [stdout] Dec 06 08:55:54.600 INFO [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 06 08:55:54.600 INFO [stdout] Dec 06 08:55:54.601 INFO [stderr] su: No module specific data is present Dec 06 08:55:55.754 INFO running `"docker" "inspect" "13fb7bcbbb8e07f5677e7685afb16c1bb890607047a2aee1f0cf741d128d7e3f"` Dec 06 08:55:56.078 INFO running `"docker" "rm" "-f" "13fb7bcbbb8e07f5677e7685afb16c1bb890607047a2aee1f0cf741d128d7e3f"` Dec 06 08:55:56.393 INFO [stdout] 13fb7bcbbb8e07f5677e7685afb16c1bb890607047a2aee1f0cf741d128d7e3f