[INFO] updating cached repository https://github.com/rhysnewell/Kallisto_Indexer
[INFO] running `"git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "-c" "remote.origin.fetch=refs/heads/*:refs/heads/*" "fetch" "origin" "--force" "--prune"`
[INFO] running `"git" "rev-parse" "HEAD"`
[INFO] [stdout] fb2da531c4e51b75f98c9782bc949a5d3d711a18
[INFO] checking rhysnewell/Kallisto_Indexer against master#bf1f2eedda4fa02b7c9347dd849ed73ddd43dedc for pr-70917
[INFO] running `"git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frhysnewell%2FKallisto_Indexer" "/workspace/builds/worker-2/source"`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/rhysnewell/Kallisto_Indexer on toolchain bf1f2eedda4fa02b7c9347dd849ed73ddd43dedc
[INFO] running `"/workspace/cargo-home/bin/cargo" "+bf1f2eedda4fa02b7c9347dd849ed73ddd43dedc" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] started tweaking git repo https://github.com/rhysnewell/Kallisto_Indexer
[INFO] finished tweaking git repo https://github.com/rhysnewell/Kallisto_Indexer
[INFO] tweaked toml for git repo https://github.com/rhysnewell/Kallisto_Indexer written to /workspace/builds/worker-2/source/Cargo.toml
[INFO] crate git repo https://github.com/rhysnewell/Kallisto_Indexer already has a lockfile, it will not be regenerated
[INFO] running `"/workspace/cargo-home/bin/cargo" "+bf1f2eedda4fa02b7c9347dd849ed73ddd43dedc" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env" "/opt/rustwide/cargo-home/bin/cargo" "+bf1f2eedda4fa02b7c9347dd849ed73ddd43dedc" "check" "--frozen" "--all" "--all-targets"`
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] [stdout] 8010108ec8360de54530ee5ecb06a3a6f102a298cfe257266223af845a614c0a
[INFO] running `"docker" "start" "-a" "8010108ec8360de54530ee5ecb06a3a6f102a298cfe257266223af845a614c0a"`
[INFO] [stderr]    Compiling serde v1.0.79
[INFO] [stderr]    Compiling bindgen v0.36.1
[INFO] [stderr]    Compiling ndarray v0.9.1
[INFO] [stderr]    Compiling bv v0.7.4
[INFO] [stderr]     Checking ieee754 v0.2.2
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]    Compiling which v1.0.5
[INFO] [stderr]    Compiling filetime v0.2.1
[INFO] [stderr]    Compiling log v0.4.5
[INFO] [stderr]    Compiling bzip2-sys v0.1.6 (https://github.com/alexcrichton/bzip2-rs.git#54aef435)
[INFO] [stderr]    Compiling libz-sys v1.0.23
[INFO] [stderr]    Compiling clang-sys v0.22.0
[INFO] [stderr]    Compiling humantime v1.1.1
[INFO] [stderr]    Compiling fs-utils v1.1.0
[INFO] [stderr]     Checking itertools v0.6.5
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking log v0.3.9
[INFO] [stderr]    Compiling lzma-sys v0.1.10
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking tempfile v3.0.4
[INFO] [stderr]    Compiling memchr v2.1.0
[INFO] [stderr]     Checking itertools-num v0.1.2
[INFO] [stderr]    Compiling libloading v0.5.0
[INFO] [stderr]     Checking colored v1.6.1
[INFO] [stderr]    Compiling thread_local v0.3.6
[INFO] [stderr]     Checking ordered-float v0.5.2
[INFO] [stderr]     Checking regex v0.2.11
[INFO] [stderr]    Compiling aho-corasick v0.6.8
[INFO] [stderr]    Compiling regex v1.0.5
[INFO] [stderr]     Checking env_logger v0.4.3
[INFO] [stderr]    Compiling env_logger v0.5.13
[INFO] [stderr]     Checking vec_map v0.8.1
[INFO] [stderr]     Checking bio-types v0.3.0
[INFO] [stderr]     Checking multimap v0.4.0
[INFO] [stderr]     Checking csv v1.0.2
[INFO] [stderr]     Checking serde_json v1.0.31
[INFO] [stderr]    Compiling clap v2.32.0
[INFO] [stderr]     Checking bio v0.20.3
[INFO] [stderr]     Checking assert_cli v0.6.3
[INFO] [stderr]    Compiling rust-htslib v0.21.1-alpha.0 (https://github.com/rust-bio/rust-htslib#1f9736ef)
[INFO] [stderr]     Checking kmer_indexer v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/lib.rs:188:13
[INFO] [stderr]     |
[INFO] [stderr] 188 |             try!(self.reader.read_line(&mut self.line));
[INFO] [stderr]     |             ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(deprecated)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/lib.rs:213:13
[INFO] [stderr]     |
[INFO] [stderr] 213 |             try!(self.reader.read_line(&mut self.line));
[INFO] [stderr]     |             ^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::collections::hash_map::Entry`
[INFO] [stderr]  --> src/genomes_and_contigs.rs:4:5
[INFO] [stderr]   |
[INFO] [stderr] 4 | use std::collections::hash_map::Entry;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::cmp::min`
[INFO] [stderr]   --> src/lib.rs:23:5
[INFO] [stderr]    |
[INFO] [stderr] 23 | use std::cmp::min;
[INFO] [stderr]    |     ^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::collections`
[INFO] [stderr]   --> src/lib.rs:24:5
[INFO] [stderr]    |
[INFO] [stderr] 24 | use std::collections;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'core::str::<impl str>::trim_right': superseded by `trim_end`
[INFO] [stderr]    --> src/lib.rs:201:14
[INFO] [stderr]     |
[INFO] [stderr] 201 |             .trim_right()
[INFO] [stderr]     |              ^^^^^^^^^^ help: replace the use of the deprecated item: `trim_end`
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'core::str::<impl str>::trim_right': superseded by `trim_end`
[INFO] [stderr]    --> src/lib.rs:207:14
[INFO] [stderr]     |
[INFO] [stderr] 207 |             .trim_right()
[INFO] [stderr]     |              ^^^^^^^^^^ help: replace the use of the deprecated item: `trim_end`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/lib.rs:276:13
[INFO] [stderr]     |
[INFO] [stderr] 276 |         let mut reader = Reader::from_file(path);
[INFO] [stderr]     |             ----^^^^^^
[INFO] [stderr]     |             |
[INFO] [stderr]     |             help: remove this `mut`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_mut)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/lib.rs:277:13
[INFO] [stderr]     |
[INFO] [stderr] 277 |         let mut name = file.to_string();
[INFO] [stderr]     |             ----^^^^
[INFO] [stderr]     |             |
[INFO] [stderr]     |             help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]   --> src/genomes_and_contigs.rs:40:17
[INFO] [stderr]    |
[INFO] [stderr] 40 |             let mut gen = genome.lines();
[INFO] [stderr]    |                 ----^^^
[INFO] [stderr]    |                 |
[INFO] [stderr]    |                 help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]   --> src/genomes_and_contigs.rs:44:17
[INFO] [stderr]    |
[INFO] [stderr] 44 |             let mut joined_genome = full_gen.join("").to_uppercase();
[INFO] [stderr]    |                 ----^^^^^^^^^^^^^
[INFO] [stderr]    |                 |
[INFO] [stderr]    |                 help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: function is never used: `find_first`
[INFO] [stderr]   --> src/genomes_and_contigs.rs:94:4
[INFO] [stderr]    |
[INFO] [stderr] 94 | fn find_first<T>(slice: &[T], element: T) -> Result<usize, &'static str>
[INFO] [stderr]    |    ^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(dead_code)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/lib.rs:188:13
[INFO] [stderr]     |
[INFO] [stderr] 188 |             try!(self.reader.read_line(&mut self.line));
[INFO] [stderr]     |             ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(deprecated)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/lib.rs:213:13
[INFO] [stderr]     |
[INFO] [stderr] 213 |             try!(self.reader.read_line(&mut self.line));
[INFO] [stderr]     |             ^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::collections::hash_map::Entry`
[INFO] [stderr]  --> src/genomes_and_contigs.rs:4:5
[INFO] [stderr]   |
[INFO] [stderr] 4 | use std::collections::hash_map::Entry;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::cmp::min`
[INFO] [stderr]   --> src/lib.rs:23:5
[INFO] [stderr]    |
[INFO] [stderr] 23 | use std::cmp::min;
[INFO] [stderr]    |     ^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::collections`
[INFO] [stderr]   --> src/lib.rs:24:5
[INFO] [stderr]    |
[INFO] [stderr] 24 | use std::collections;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'core::str::<impl str>::trim_right': superseded by `trim_end`
[INFO] [stderr]    --> src/lib.rs:201:14
[INFO] [stderr]     |
[INFO] [stderr] 201 |             .trim_right()
[INFO] [stderr]     |              ^^^^^^^^^^ help: replace the use of the deprecated item: `trim_end`
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'core::str::<impl str>::trim_right': superseded by `trim_end`
[INFO] [stderr]    --> src/lib.rs:207:14
[INFO] [stderr]     |
[INFO] [stderr] 207 |             .trim_right()
[INFO] [stderr]     |              ^^^^^^^^^^ help: replace the use of the deprecated item: `trim_end`
[INFO] [stderr] 
[INFO] [stderr] error[E0599]: no method named `genome_of_contig` found for struct `genomes_and_contigs::GenomesAndContigs` in the current scope
[INFO] [stderr]    --> src/lib.rs:303:32
[INFO] [stderr]     |
[INFO] [stderr] 303 |             *(contig_to_genome.genome_of_contig(&String::from("contig1")).unwrap()));
[INFO] [stderr]     |                                ^^^^^^^^^^^^^^^^ method not found in `genomes_and_contigs::GenomesAndContigs`
[INFO] [stderr]     | 
[INFO] [stderr]    ::: src/genomes_and_contigs.rs:8:1
[INFO] [stderr]     |
[INFO] [stderr] 8   | pub struct GenomesAndContigs {
[INFO] [stderr]     | ---------------------------- method `genome_of_contig` not found for this
[INFO] [stderr] 
[INFO] [stderr] error[E0599]: no method named `genome_of_contig` found for struct `genomes_and_contigs::GenomesAndContigs` in the current scope
[INFO] [stderr]    --> src/lib.rs:309:63
[INFO] [stderr]     |
[INFO] [stderr] 309 |         assert_eq!(String::from("genome1"), *contig_to_genome.genome_of_contig(&String::from("seq1")).unwrap());
[INFO] [stderr]     |                                                               ^^^^^^^^^^^^^^^^ method not found in `genomes_and_contigs::GenomesAndContigs`
[INFO] [stderr]     | 
[INFO] [stderr]    ::: src/genomes_and_contigs.rs:8:1
[INFO] [stderr]     |
[INFO] [stderr] 8   | pub struct GenomesAndContigs {
[INFO] [stderr]     | ---------------------------- method `genome_of_contig` not found for this
[INFO] [stderr] 
[INFO] [stderr] error[E0599]: no method named `genome_of_contig` found for struct `genomes_and_contigs::GenomesAndContigs` in the current scope
[INFO] [stderr]    --> src/lib.rs:310:63
[INFO] [stderr]     |
[INFO] [stderr] 310 |         assert_eq!(String::from("genome1"), *contig_to_genome.genome_of_contig(&String::from("seq2")).unwrap());
[INFO] [stderr]     |                                                               ^^^^^^^^^^^^^^^^ method not found in `genomes_and_contigs::GenomesAndContigs`
[INFO] [stderr]     | 
[INFO] [stderr]    ::: src/genomes_and_contigs.rs:8:1
[INFO] [stderr]     |
[INFO] [stderr] 8   | pub struct GenomesAndContigs {
[INFO] [stderr]     | ---------------------------- method `genome_of_contig` not found for this
[INFO] [stderr] 
[INFO] [stderr] error: aborting due to 3 previous errors
[INFO] [stderr] 
[INFO] [stderr] For more information about this error, try `rustc --explain E0599`.
[INFO] [stderr] error: could not compile `kmer_indexer`.
[INFO] [stderr] 
[INFO] [stderr] To learn more, run the command again with --verbose.
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] [stderr] warning: unused `#[macro_use]` import
[INFO] [stderr]   --> src/main.rs:11:1
[INFO] [stderr]    |
[INFO] [stderr] 11 | #[macro_use]
[INFO] [stderr]    | ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `log::LogLevelFilter`
[INFO] [stderr]   --> src/main.rs:13:5
[INFO] [stderr]    |
[INFO] [stderr] 13 | use log::LogLevelFilter;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `env_logger::LogBuilder`
[INFO] [stderr]   --> src/main.rs:15:5
[INFO] [stderr]    |
[INFO] [stderr] 15 | use env_logger::LogBuilder;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `kmer_indexer::genomes_and_contigs`
[INFO] [stderr]   --> src/main.rs:17:5
[INFO] [stderr]    |
[INFO] [stderr] 17 | use kmer_indexer::genomes_and_contigs;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused imports: `tempdir`, `tempfile`
[INFO] [stderr]   --> src/main.rs:18:16
[INFO] [stderr]    |
[INFO] [stderr] 18 | use tempfile::{tempfile, tempdir, Builder};
[INFO] [stderr]    |                ^^^^^^^^  ^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `self`
[INFO] [stderr]   --> src/main.rs:19:15
[INFO] [stderr]    |
[INFO] [stderr] 19 | use std::io::{self, Write, Read};
[INFO] [stderr]    |               ^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::env`
[INFO] [stderr]   --> src/main.rs:20:5
[INFO] [stderr]    |
[INFO] [stderr] 20 | use std::env;
[INFO] [stderr]    |     ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `self`
[INFO] [stderr]   --> src/main.rs:22:20
[INFO] [stderr]    |
[INFO] [stderr] 22 | use std::process::{self, Command};
[INFO] [stderr]    |                    ^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::path::Path`
[INFO] [stderr]   --> src/main.rs:24:5
[INFO] [stderr]    |
[INFO] [stderr] 24 | use std::path::Path;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::error::Error`
[INFO] [stderr]   --> src/main.rs:25:5
[INFO] [stderr]    |
[INFO] [stderr] 25 | use std::error::Error;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::ffi::OsString`
[INFO] [stderr]   --> src/main.rs:26:5
[INFO] [stderr]    |
[INFO] [stderr] 26 | use std::ffi::OsString;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `self`
[INFO] [stderr]   --> src/main.rs:27:15
[INFO] [stderr]    |
[INFO] [stderr] 27 | use std::fs::{self, File};
[INFO] [stderr]    |               ^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused imports: `ReaderBuilder`, `Writer`
[INFO] [stderr]   --> src/main.rs:28:11
[INFO] [stderr]    |
[INFO] [stderr] 28 | use csv::{Writer, ReaderBuilder};
[INFO] [stderr]    |           ^^^^^^  ^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused `#[macro_use]` import
[INFO] [stderr]   --> src/main.rs:11:1
[INFO] [stderr]    |
[INFO] [stderr] 11 | #[macro_use]
[INFO] [stderr]    | ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(unused_imports)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `log::LogLevelFilter`
[INFO] [stderr]   --> src/main.rs:13:5
[INFO] [stderr]    |
[INFO] [stderr] 13 | use log::LogLevelFilter;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `env_logger::LogBuilder`
[INFO] [stderr]   --> src/main.rs:15:5
[INFO] [stderr]    |
[INFO] [stderr] 15 | use env_logger::LogBuilder;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `kmer_indexer::genomes_and_contigs`
[INFO] [stderr]   --> src/main.rs:17:5
[INFO] [stderr]    |
[INFO] [stderr] 17 | use kmer_indexer::genomes_and_contigs;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused imports: `tempdir`, `tempfile`
[INFO] [stderr]   --> src/main.rs:18:16
[INFO] [stderr]    |
[INFO] [stderr] 18 | use tempfile::{tempfile, tempdir, Builder};
[INFO] [stderr]    |                ^^^^^^^^  ^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `self`
[INFO] [stderr]   --> src/main.rs:19:15
[INFO] [stderr]    |
[INFO] [stderr] 19 | use std::io::{self, Write, Read};
[INFO] [stderr]    |               ^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::env`
[INFO] [stderr]   --> src/main.rs:20:5
[INFO] [stderr]    |
[INFO] [stderr] 20 | use std::env;
[INFO] [stderr]    |     ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `self`
[INFO] [stderr]   --> src/main.rs:22:20
[INFO] [stderr]    |
[INFO] [stderr] 22 | use std::process::{self, Command};
[INFO] [stderr]    |                    ^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::path::Path`
[INFO] [stderr]   --> src/main.rs:24:5
[INFO] [stderr]    |
[INFO] [stderr] 24 | use std::path::Path;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::error::Error`
[INFO] [stderr]   --> src/main.rs:25:5
[INFO] [stderr]    |
[INFO] [stderr] 25 | use std::error::Error;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::ffi::OsString`
[INFO] [stderr]   --> src/main.rs:26:5
[INFO] [stderr]    |
[INFO] [stderr] 26 | use std::ffi::OsString;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `self`
[INFO] [stderr]   --> src/main.rs:27:15
[INFO] [stderr]    |
[INFO] [stderr] 27 | use std::fs::{self, File};
[INFO] [stderr]    |               ^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused imports: `ReaderBuilder`, `Writer`
[INFO] [stderr]   --> src/main.rs:28:11
[INFO] [stderr]    |
[INFO] [stderr] 28 | use csv::{Writer, ReaderBuilder};
[INFO] [stderr]    |           ^^^^^^  ^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `genomes_string`
[INFO] [stderr]    --> src/main.rs:145:21
[INFO] [stderr]     |
[INFO] [stderr] 145 |             let mut genomes_string = String::new();
[INFO] [stderr]     |                     ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_genomes_string`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable `output` is assigned to, but never used
[INFO] [stderr]    --> src/main.rs:199:13
[INFO] [stderr]     |
[INFO] [stderr] 199 |     let mut output;
[INFO] [stderr]     |             ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: consider using `_output` instead
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `output` is never read
[INFO] [stderr]    --> src/main.rs:201:9
[INFO] [stderr]     |
[INFO] [stderr] 201 |         output = Command::new("Bifrost")
[INFO] [stderr]     |         ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_assignments)]` on by default
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `output` is never read
[INFO] [stderr]    --> src/main.rs:214:9
[INFO] [stderr]     |
[INFO] [stderr] 214 |         output = Command::new("Bifrost")
[INFO] [stderr]     |         ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/main.rs:145:17
[INFO] [stderr]     |
[INFO] [stderr] 145 |             let mut genomes_string = String::new();
[INFO] [stderr]     |                 ----^^^^^^^^^^^^^^
[INFO] [stderr]     |                 |
[INFO] [stderr]     |                 help: remove this `mut`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_mut)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/main.rs:199:9
[INFO] [stderr]     |
[INFO] [stderr] 199 |     let mut output;
[INFO] [stderr]     |         ----^^^^^^
[INFO] [stderr]     |         |
[INFO] [stderr]     |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `genomes_string`
[INFO] [stderr]    --> src/main.rs:145:21
[INFO] [stderr]     |
[INFO] [stderr] 145 |             let mut genomes_string = String::new();
[INFO] [stderr]     |                     ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_genomes_string`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_variables)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable `output` is assigned to, but never used
[INFO] [stderr]    --> src/main.rs:199:13
[INFO] [stderr]     |
[INFO] [stderr] 199 |     let mut output;
[INFO] [stderr]     |             ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: consider using `_output` instead
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `output` is never read
[INFO] [stderr]    --> src/main.rs:201:9
[INFO] [stderr]     |
[INFO] [stderr] 201 |         output = Command::new("Bifrost")
[INFO] [stderr]     |         ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_assignments)]` on by default
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `output` is never read
[INFO] [stderr]    --> src/main.rs:214:9
[INFO] [stderr]     |
[INFO] [stderr] 214 |         output = Command::new("Bifrost")
[INFO] [stderr]     |         ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/main.rs:240:13
[INFO] [stderr]     |
[INFO] [stderr] 240 |         let mut output;
[INFO] [stderr]     |             ----^^^^^^
[INFO] [stderr]     |             |
[INFO] [stderr]     |             help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:47:17
[INFO] [stderr]    |
[INFO] [stderr] 47 |                 run_kallisto(genomes_string, m.clone());
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(unused_must_use)]` on by default
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:54:17
[INFO] [stderr]    |
[INFO] [stderr] 54 |                 file_path.read_to_string(&mut contents);
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:82:17
[INFO] [stderr]    |
[INFO] [stderr] 82 |                 run_kallisto(genomes_string, m.clone());
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:91:13
[INFO] [stderr]    |
[INFO] [stderr] 91 |             file_path.read_to_string(&mut contents);
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:99:13
[INFO] [stderr]    |
[INFO] [stderr] 99 |             rep_path.read_to_string(&mut rep_contents);
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: variable `RepRecord` should have a snake case name
[INFO] [stderr]    --> src/main.rs:105:21
[INFO] [stderr]     |
[INFO] [stderr] 105 |             let mut RepRecord: HashSet<String> = HashSet::new();
[INFO] [stderr]     |                     ^^^^^^^^^ help: convert the identifier to snake case: `rep_record`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(non_snake_case)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:130:17
[INFO] [stderr]     |
[INFO] [stderr] 130 |                 gen_file.write_all(f.as_bytes());
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:132:13
[INFO] [stderr]     |
[INFO] [stderr] 132 |             gen_file.flush();
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:136:17
[INFO] [stderr]     |
[INFO] [stderr] 136 |                 rep_file.write_all(f.as_bytes());
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:138:13
[INFO] [stderr]     |
[INFO] [stderr] 138 |             gen_file.flush();
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:140:13
[INFO] [stderr]     |
[INFO] [stderr] 140 |             run_bifrost(m.clone());
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:156:17
[INFO] [stderr]     |
[INFO] [stderr] 156 |                 file_path.read_to_string(&mut contents);
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/main.rs:145:17
[INFO] [stderr]     |
[INFO] [stderr] 145 |             let mut genomes_string = String::new();
[INFO] [stderr]     |                 ----^^^^^^^^^^^^^^
[INFO] [stderr]     |                 |
[INFO] [stderr]     |                 help: remove this `mut`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_mut)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/main.rs:199:9
[INFO] [stderr]     |
[INFO] [stderr] 199 |     let mut output;
[INFO] [stderr]     |         ----^^^^^^
[INFO] [stderr]     |         |
[INFO] [stderr]     |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/main.rs:240:13
[INFO] [stderr]     |
[INFO] [stderr] 240 |         let mut output;
[INFO] [stderr]     |             ----^^^^^^
[INFO] [stderr]     |             |
[INFO] [stderr]     |             help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:47:17
[INFO] [stderr]    |
[INFO] [stderr] 47 |                 run_kallisto(genomes_string, m.clone());
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(unused_must_use)]` on by default
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:54:17
[INFO] [stderr]    |
[INFO] [stderr] 54 |                 file_path.read_to_string(&mut contents);
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:82:17
[INFO] [stderr]    |
[INFO] [stderr] 82 |                 run_kallisto(genomes_string, m.clone());
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:91:13
[INFO] [stderr]    |
[INFO] [stderr] 91 |             file_path.read_to_string(&mut contents);
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]   --> src/main.rs:99:13
[INFO] [stderr]    |
[INFO] [stderr] 99 |             rep_path.read_to_string(&mut rep_contents);
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: variable `RepRecord` should have a snake case name
[INFO] [stderr]    --> src/main.rs:105:21
[INFO] [stderr]     |
[INFO] [stderr] 105 |             let mut RepRecord: HashSet<String> = HashSet::new();
[INFO] [stderr]     |                     ^^^^^^^^^ help: convert the identifier to snake case: `rep_record`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(non_snake_case)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:130:17
[INFO] [stderr]     |
[INFO] [stderr] 130 |                 gen_file.write_all(f.as_bytes());
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:132:13
[INFO] [stderr]     |
[INFO] [stderr] 132 |             gen_file.flush();
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:136:17
[INFO] [stderr]     |
[INFO] [stderr] 136 |                 rep_file.write_all(f.as_bytes());
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:138:13
[INFO] [stderr]     |
[INFO] [stderr] 138 |             gen_file.flush();
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:140:13
[INFO] [stderr]     |
[INFO] [stderr] 140 |             run_bifrost(m.clone());
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] warning: unused `std::result::Result` that must be used
[INFO] [stderr]    --> src/main.rs:156:17
[INFO] [stderr]     |
[INFO] [stderr] 156 |                 file_path.read_to_string(&mut contents);
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: this `Result` may be an `Err` variant, which should be handled
[INFO] [stderr] 
[INFO] [stderr] error: build failed
[INFO] running `"docker" "inspect" "8010108ec8360de54530ee5ecb06a3a6f102a298cfe257266223af845a614c0a"`
[INFO] running `"docker" "rm" "-f" "8010108ec8360de54530ee5ecb06a3a6f102a298cfe257266223af845a614c0a"`
[INFO] [stdout] 8010108ec8360de54530ee5ecb06a3a6f102a298cfe257266223af845a614c0a
