[INFO] updating cached repository rhysnewell/Kallisto_Indexer
[INFO] running `"git" "fetch" "--all"`
[INFO] [stdout] Fetching origin
[INFO] [stderr] From git://github.com/rhysnewell/Kallisto_Indexer
[INFO] [stderr]  * branch            HEAD       -> FETCH_HEAD
[INFO] running `"git" "clone" "work/cache/sources/gh/rhysnewell/Kallisto_Indexer" "work/ex/pr-61874/sources/master#9f06855064ed06a50c496577b21ca50f92a2e67d/gh/rhysnewell/Kallisto_Indexer"`
[INFO] [stderr] Cloning into 'work/ex/pr-61874/sources/master#9f06855064ed06a50c496577b21ca50f92a2e67d/gh/rhysnewell/Kallisto_Indexer'...
[INFO] [stderr] done.
[INFO] running `"git" "clone" "work/cache/sources/gh/rhysnewell/Kallisto_Indexer" "work/ex/pr-61874/sources/try#d3301713b54af69ca9de941a8c6b0d8287dbd6df/gh/rhysnewell/Kallisto_Indexer"`
[INFO] [stderr] Cloning into 'work/ex/pr-61874/sources/try#d3301713b54af69ca9de941a8c6b0d8287dbd6df/gh/rhysnewell/Kallisto_Indexer'...
[INFO] [stderr] done.
[INFO] running `"git" "rev-parse" "HEAD"`
[INFO] [stdout] fb2da531c4e51b75f98c9782bc949a5d3d711a18
[INFO] sha for GitHub repo rhysnewell/Kallisto_Indexer: fb2da531c4e51b75f98c9782bc949a5d3d711a18
[INFO] validating manifest of rhysnewell/Kallisto_Indexer on toolchain master#9f06855064ed06a50c496577b21ca50f92a2e67d
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+9f06855064ed06a50c496577b21ca50f92a2e67d-alt" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] validating manifest of rhysnewell/Kallisto_Indexer on toolchain try#d3301713b54af69ca9de941a8c6b0d8287dbd6df
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+d3301713b54af69ca9de941a8c6b0d8287dbd6df-alt" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] started frobbing rhysnewell/Kallisto_Indexer
[INFO] finished frobbing rhysnewell/Kallisto_Indexer
[INFO] frobbed toml for rhysnewell/Kallisto_Indexer written to work/ex/pr-61874/sources/master#9f06855064ed06a50c496577b21ca50f92a2e67d/gh/rhysnewell/Kallisto_Indexer/Cargo.toml
[INFO] started frobbing rhysnewell/Kallisto_Indexer
[INFO] finished frobbing rhysnewell/Kallisto_Indexer
[INFO] frobbed toml for rhysnewell/Kallisto_Indexer written to work/ex/pr-61874/sources/try#d3301713b54af69ca9de941a8c6b0d8287dbd6df/gh/rhysnewell/Kallisto_Indexer/Cargo.toml
[INFO] crate rhysnewell/Kallisto_Indexer already has a lockfile, it will not be regenerated
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+9f06855064ed06a50c496577b21ca50f92a2e67d-alt" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+d3301713b54af69ca9de941a8c6b0d8287dbd6df-alt" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] checking rhysnewell/Kallisto_Indexer against try#d3301713b54af69ca9de941a8c6b0d8287dbd6df for pr-61874
[INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-61874/worker-5/try#d3301713b54af69ca9de941a8c6b0d8287dbd6df:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/pr-61874/sources/try#d3301713b54af69ca9de941a8c6b0d8287dbd6df/gh/rhysnewell/Kallisto_Indexer:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+d3301713b54af69ca9de941a8c6b0d8287dbd6df-alt" "check" "--frozen" "--all" "--all-targets"`
[INFO] [stdout] 8726db3724267d4fe581da87a2ebf09ee9afe41e2a0fb5610e21b85a7cb2a1ab
[INFO] running `"docker" "start" "-a" "8726db3724267d4fe581da87a2ebf09ee9afe41e2a0fb5610e21b85a7cb2a1ab"`
[INFO] [stderr]    Compiling bindgen v0.36.1
[INFO] [stderr]    Compiling bv v0.7.4
[INFO] [stderr]    Compiling ndarray v0.9.1
[INFO] [stderr]     Checking ieee754 v0.2.2
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking environment v0.1.1
[INFO] [stderr]    Compiling filetime v0.2.1
[INFO] [stderr]    Compiling bzip2-sys v0.1.6 (https://github.com/alexcrichton/bzip2-rs.git#54aef435)
[INFO] [stderr]    Compiling clang-sys v0.22.0
[INFO] [stderr]    Compiling fs-utils v1.1.0
[INFO] [stderr]    Compiling libz-sys v1.0.23
[INFO] [stderr]     Checking itertools v0.6.5
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling lzma-sys v0.1.10
[INFO] [stderr]    Compiling libloading v0.5.0
[INFO] [stderr]     Checking itertools-num v0.1.2
[INFO] [stderr]    Compiling syn v0.15.6
[INFO] [stderr]     Checking csv-core v0.1.4
[INFO] [stderr]     Checking env_logger v0.4.3
[INFO] [stderr]    Compiling serde_derive v1.0.79
[INFO] [stderr]    Compiling serde v1.0.79
[INFO] [stderr]     Checking multimap v0.4.0
[INFO] [stderr]     Checking bio-types v0.3.0
[INFO] [stderr]     Checking csv v1.0.2
[INFO] [stderr]     Checking vec_map v0.8.1
[INFO] [stderr]     Checking serde_json v1.0.31
[INFO] [stderr]     Checking 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/crater/workdir)
[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]     = note: #[warn(deprecated)] on by default
[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: 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]     = note: #[warn(deprecated)] on by default
[INFO] [stderr] 
[INFO] [stderr] error[E0599]: no method named `genome_of_contig` found for type `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]     |                                ^^^^^^^^^^^^^^^^
[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] 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 type `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]     |                                                               ^^^^^^^^^^^^^^^^
[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 type `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]     |                                                               ^^^^^^^^^^^^^^^^
[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] warning: build failed, waiting for other jobs to finish...
[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:94:1
[INFO] [stderr]     |
[INFO] [stderr] 94  | / fn find_first<T>(slice: &[T], element: T) -> Result<usize, &'static str>
[INFO] [stderr] 95  | |     where T: std::cmp::PartialEq<T> {
[INFO] [stderr] 96  | |
[INFO] [stderr] 97  | |     let mut index: usize = 0;
[INFO] [stderr] ...   |
[INFO] [stderr] 105 | |     return Err("Element not found in slice")
[INFO] [stderr] 106 | | }
[INFO] [stderr]     | |_^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(dead_code)] on by default
[INFO] [stderr] 
[INFO] [stderr] error: build failed
[INFO] running `"docker" "inspect" "8726db3724267d4fe581da87a2ebf09ee9afe41e2a0fb5610e21b85a7cb2a1ab"`
[INFO] running `"docker" "rm" "-f" "8726db3724267d4fe581da87a2ebf09ee9afe41e2a0fb5610e21b85a7cb2a1ab"`
[INFO] [stdout] 8726db3724267d4fe581da87a2ebf09ee9afe41e2a0fb5610e21b85a7cb2a1ab