[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] testing rhysnewell/Kallisto_Indexer against beta-2020-06-03 for beta-1.45-1 [INFO] running `"git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frhysnewell%2FKallisto_Indexer" "/workspace/builds/worker-9/source"` [INFO] [stderr] Cloning into '/workspace/builds/worker-9/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/rhysnewell/Kallisto_Indexer on toolchain beta-2020-06-03 [INFO] running `"/workspace/cargo-home/bin/cargo" "+beta-2020-06-03" "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-9/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" "+beta-2020-06-03" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/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=warn" "-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" "+beta-2020-06-03" "build" "--frozen"` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] a2e20824f5687786b51831c06d7821d09c4344e6c0fdc495ff061e2fa0ba7c8d [INFO] running `"docker" "start" "-a" "a2e20824f5687786b51831c06d7821d09c4344e6c0fdc495ff061e2fa0ba7c8d"` [INFO] [stderr] sudo: setrlimit(RLIMIT_CORE): Operation not permitted [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] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling ieee754 v0.2.2 [INFO] [stderr] Compiling libloading v0.5.0 [INFO] [stderr] Compiling regex-syntax v0.5.6 [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 which v1.0.5 [INFO] [stderr] Compiling itertools v0.6.5 [INFO] [stderr] Compiling libz-sys v1.0.23 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling fs-utils v1.1.0 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling log v0.3.9 [INFO] [stderr] Compiling nix v0.11.0 [INFO] [stderr] Compiling bit-set v0.4.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling tempfile v3.0.4 [INFO] [stderr] Compiling lzma-sys v0.1.10 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling itertools-num v0.1.2 [INFO] [stderr] Compiling ordered-float v0.5.2 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling env_logger v0.4.3 [INFO] [stderr] Compiling vec_map v0.8.1 [INFO] [stderr] Compiling bio-types v0.3.0 [INFO] [stderr] Compiling csv v1.0.2 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling clap v2.32.0 [INFO] [stderr] Compiling bio v0.20.3 [INFO] [stderr] Compiling rust-htslib v0.21.1-alpha.0 (https://github.com/rust-bio/rust-htslib#1f9736ef) [INFO] [stderr] Compiling 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] 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] warning: 12 warnings emitted [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:145:17 [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:199:9 [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: 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 = 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: 32 warnings emitted [INFO] [stderr] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 52s [INFO] running `"docker" "inspect" "a2e20824f5687786b51831c06d7821d09c4344e6c0fdc495ff061e2fa0ba7c8d"` [INFO] running `"docker" "rm" "-f" "a2e20824f5687786b51831c06d7821d09c4344e6c0fdc495ff061e2fa0ba7c8d"` [INFO] [stdout] a2e20824f5687786b51831c06d7821d09c4344e6c0fdc495ff061e2fa0ba7c8d [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/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=warn" "-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" "+beta-2020-06-03" "test" "--frozen" "--no-run"` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] d29f00748102fac0c15c536b83fc0a24a7badc385048c7a5870c3b283b019081 [INFO] running `"docker" "start" "-a" "d29f00748102fac0c15c536b83fc0a24a7badc385048c7a5870c3b283b019081"` [INFO] [stderr] sudo: setrlimit(RLIMIT_CORE): Operation not permitted [INFO] [stderr] Compiling environment v0.1.1 [INFO] [stderr] Compiling serde_json v1.0.31 [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] warning: 12 warnings emitted [INFO] [stderr] [INFO] [stderr] Compiling assert_cli v0.6.3 [INFO] [stderr] Compiling 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] 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:145:17 [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:199:9 [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: 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 = 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[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; 7 warnings emitted [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: 32 warnings emitted [INFO] [stderr] [INFO] [stderr] error: build failed [INFO] running `"docker" "inspect" "d29f00748102fac0c15c536b83fc0a24a7badc385048c7a5870c3b283b019081"` [INFO] running `"docker" "rm" "-f" "d29f00748102fac0c15c536b83fc0a24a7badc385048c7a5870c3b283b019081"` [INFO] [stdout] d29f00748102fac0c15c536b83fc0a24a7badc385048c7a5870c3b283b019081