[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 try#1a608893c03d7722effeb0058e82770bd36b4b3c for pr-66504-1 [INFO] running `"git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frhysnewell%2FKallisto_Indexer" "/workspace/builds/worker-12/source"` [INFO] [stderr] Cloning into '/workspace/builds/worker-12/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/rhysnewell/Kallisto_Indexer on toolchain 1a608893c03d7722effeb0058e82770bd36b4b3c [INFO] running `"/workspace/cargo-home/bin/cargo" "+1a608893c03d7722effeb0058e82770bd36b4b3c" "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-12/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" "+1a608893c03d7722effeb0058e82770bd36b4b3c" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-12/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-12/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" "+1a608893c03d7722effeb0058e82770bd36b4b3c" "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] 624e06a1223dba71c3b3af6cd6bfa3eb5a840fd378febed1d4879c252d428ed2 [INFO] running `"docker" "start" "-a" "624e06a1223dba71c3b3af6cd6bfa3eb5a840fd378febed1d4879c252d428ed2"` [INFO] [stderr] Compiling serde v1.0.79 [INFO] [stderr] Compiling unicode-width v0.1.5 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling ndarray v0.9.1 [INFO] [stderr] Compiling bv v0.7.4 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking ieee754 v0.2.2 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling filetime v0.2.1 [INFO] [stderr] Compiling humantime v1.1.1 [INFO] [stderr] Compiling proc-macro2 v0.3.5 [INFO] [stderr] Compiling libz-sys v1.0.23 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Compiling bzip2-sys v0.1.6 (https://github.com/alexcrichton/bzip2-rs.git#54aef435) [INFO] [stderr] Compiling fs-utils v1.1.0 [INFO] [stderr] Checking itertools v0.6.5 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Compiling textwrap v0.10.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling nom v3.2.1 [INFO] [stderr] Checking itertools-num v0.1.2 [INFO] [stderr] Compiling libloading v0.5.0 [INFO] [stderr] Compiling lzma-sys v0.1.10 [INFO] [stderr] Checking csv-core v0.1.4 [INFO] [stderr] Checking ordered-float v0.5.2 [INFO] [stderr] Compiling synstructure v0.9.0 [INFO] [stderr] Checking env_logger v0.4.3 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling quote v0.5.2 [INFO] [stderr] Compiling failure_derive v0.1.2 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Checking failure v0.1.2 [INFO] [stderr] Checking vec_map v0.8.1 [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 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/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::::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::::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: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 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] | ^^^^^^^^^^^^^^^^ 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 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] | ^^^^^^^^^^^^^^^^ 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] warning: build failed, waiting for other jobs to finish... [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::::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::::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(slice: &[T], element: T) -> Result [INFO] [stderr] | ^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] error: build failed [INFO] running `"docker" "inspect" "624e06a1223dba71c3b3af6cd6bfa3eb5a840fd378febed1d4879c252d428ed2"` [INFO] running `"docker" "rm" "-f" "624e06a1223dba71c3b3af6cd6bfa3eb5a840fd378febed1d4879c252d428ed2"` [INFO] [stdout] 624e06a1223dba71c3b3af6cd6bfa3eb5a840fd378febed1d4879c252d428ed2