[INFO] cloning repository https://github.com/rhysnewell/Kallisto_Indexer [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/rhysnewell/Kallisto_Indexer" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frhysnewell%2FKallisto_Indexer", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frhysnewell%2FKallisto_Indexer'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] fb2da531c4e51b75f98c9782bc949a5d3d711a18 [INFO] checking rhysnewell/Kallisto_Indexer against try#ffa4a0215752773248fb0f0a8092f1c3e7907e9e for pr-75585 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frhysnewell%2FKallisto_Indexer" "/workspace/builds/worker-10/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-10/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/rhysnewell/Kallisto_Indexer on toolchain ffa4a0215752773248fb0f0a8092f1c3e7907e9e [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+ffa4a0215752773248fb0f0a8092f1c3e7907e9e" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [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-10/source/Cargo.toml [INFO] crate git repo https://github.com/rhysnewell/Kallisto_Indexer already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+ffa4a0215752773248fb0f0a8092f1c3e7907e9e" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating git repository `https://github.com/rust-bio/rust-htslib` [INFO] [stderr] Updating git submodule `https://github.com/samtools/htslib.git` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded itertools-num v0.1.2 [INFO] [stderr] Downloaded clang-sys v0.22.0 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded bindgen v0.36.1 [INFO] [stderr] Downloaded ieee754 v0.2.2 [INFO] [stderr] Downloaded fs-utils v1.1.0 [INFO] [stderr] Downloaded bv v0.7.4 [INFO] [stderr] Downloaded bio-types v0.3.0 [INFO] [stderr] Downloaded libz-sys v1.0.23 [INFO] [stderr] Downloaded ndarray v0.9.1 [INFO] [stderr] Downloaded lzma-sys v0.1.10 [INFO] [stderr] Downloaded bio v0.20.3 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/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" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+ffa4a0215752773248fb0f0a8092f1c3e7907e9e" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 5329dd5a83e1d165e8627533357c22b887a3bd4597a87ace293fb868a910b16d [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "5329dd5a83e1d165e8627533357c22b887a3bd4597a87ace293fb868a910b16d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "5329dd5a83e1d165e8627533357c22b887a3bd4597a87ace293fb868a910b16d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5329dd5a83e1d165e8627533357c22b887a3bd4597a87ace293fb868a910b16d", kill_on_drop: false }` [INFO] [stdout] 5329dd5a83e1d165e8627533357c22b887a3bd4597a87ace293fb868a910b16d [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/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" "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" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+ffa4a0215752773248fb0f0a8092f1c3e7907e9e" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 086d4c433b99b6819bb59dc9d3bc1a4993e08cebab878bbfab8e140af013f8ec [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "086d4c433b99b6819bb59dc9d3bc1a4993e08cebab878bbfab8e140af013f8ec", kill_on_drop: false }` [INFO] [stderr] Compiling cc v1.0.25 [INFO] [stderr] Checking libc v0.2.43 [INFO] [stderr] Compiling serde v1.0.79 [INFO] [stderr] Compiling cfg-if v0.1.5 [INFO] [stderr] Compiling ucd-util v0.1.1 [INFO] [stderr] Compiling num-traits v0.2.6 [INFO] [stderr] Compiling regex v1.0.5 [INFO] [stderr] Compiling utf8-ranges v1.0.1 [INFO] [stderr] Compiling quick-error v1.2.2 [INFO] [stderr] Compiling unicode-width v0.1.5 [INFO] [stderr] Compiling bitflags v1.0.4 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling strsim v0.7.0 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling termcolor v1.0.4 [INFO] [stderr] Compiling matrixmultiply v0.1.14 [INFO] [stderr] Checking void v1.0.2 [INFO] [stderr] Checking either v1.5.0 [INFO] [stderr] Compiling bv v0.7.4 [INFO] [stderr] Checking rawpointer v0.1.0 [INFO] [stderr] Compiling ndarray v0.9.1 [INFO] [stderr] Checking bit-vec v0.4.4 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking ieee754 v0.2.2 [INFO] [stderr] Checking approx v0.1.1 [INFO] [stderr] Checking bytecount v0.3.2 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking environment v0.1.1 [INFO] [stderr] Compiling lazy_static v1.1.0 [INFO] [stderr] Compiling memchr v2.1.0 [INFO] [stderr] Compiling proc-macro2 v0.3.5 [INFO] [stderr] Checking log v0.4.5 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling atty v0.2.11 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Compiling textwrap v0.10.0 [INFO] [stderr] Compiling filetime v0.2.1 [INFO] [stderr] Compiling humantime v1.1.1 [INFO] [stderr] Compiling fs-utils v1.1.0 [INFO] [stderr] Compiling regex-syntax v0.6.2 [INFO] [stderr] Compiling regex-syntax v0.5.6 [INFO] [stderr] Checking unreachable v1.0.0 [INFO] [stderr] Checking itertools v0.6.5 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking rand v0.5.5 [INFO] [stderr] Compiling proc-macro2 v0.4.19 [INFO] [stderr] Checking bit-set v0.4.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking log v0.3.9 [INFO] [stderr] Compiling nom v3.2.1 [INFO] [stderr] Compiling quote v0.5.2 [INFO] [stderr] Checking nix v0.11.0 [INFO] [stderr] Checking url v1.7.1 [INFO] [stderr] Checking thread_local v0.3.6 [INFO] [stderr] Checking colored v1.6.1 [INFO] [stderr] Compiling quote v0.6.8 [INFO] [stderr] Checking aho-corasick v0.6.8 [INFO] [stderr] Checking csv-core v0.1.4 [INFO] [stderr] Compiling syn v0.15.6 [INFO] [stderr] Compiling syn v0.14.9 [INFO] [stderr] Compiling libloading v0.5.0 [INFO] [stderr] Compiling lzma-sys v0.1.10 [INFO] [stderr] Compiling libz-sys v1.0.23 [INFO] [stderr] Compiling bzip2-sys v0.1.6 (https://github.com/alexcrichton/bzip2-rs.git#54aef435) [INFO] [stderr] Compiling backtrace-sys v0.1.24 [INFO] [stderr] Checking tempfile v3.0.4 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Checking num-traits v0.1.43 [INFO] [stderr] Checking num-complex v0.1.43 [INFO] [stderr] Checking itertools-num v0.1.2 [INFO] [stderr] Checking num-integer v0.1.39 [INFO] [stderr] Checking ordered-float v0.5.2 [INFO] [stderr] Checking regex v0.2.11 [INFO] [stderr] Checking backtrace v0.3.9 [INFO] [stderr] Checking env_logger v0.4.3 [INFO] [stderr] Compiling synstructure v0.9.0 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling serde_derive v1.0.79 [INFO] [stderr] Compiling failure_derive v0.1.2 [INFO] [stderr] Checking failure v0.1.2 [INFO] [stderr] Checking vec_map v0.8.1 [INFO] [stderr] Checking csv v1.0.2 [INFO] [stderr] Checking multimap v0.4.0 [INFO] [stderr] Checking bio-types v0.3.0 [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] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/lib.rs:188:13 [INFO] [stdout] | [INFO] [stdout] 188 | try!(self.reader.read_line(&mut self.line)); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/lib.rs:213:13 [INFO] [stdout] | [INFO] [stdout] 213 | try!(self.reader.read_line(&mut self.line)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::hash_map::Entry` [INFO] [stdout] --> src/genomes_and_contigs.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::collections::hash_map::Entry; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::cmp::min` [INFO] [stdout] --> src/lib.rs:23:5 [INFO] [stdout] | [INFO] [stdout] 23 | use std::cmp::min; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections` [INFO] [stdout] --> src/lib.rs:24:5 [INFO] [stdout] | [INFO] [stdout] 24 | use std::collections; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/lib.rs:188:13 [INFO] [stdout] | [INFO] [stdout] 188 | try!(self.reader.read_line(&mut self.line)); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/lib.rs:213:13 [INFO] [stdout] | [INFO] [stdout] 213 | try!(self.reader.read_line(&mut self.line)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::hash_map::Entry` [INFO] [stdout] --> src/genomes_and_contigs.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::collections::hash_map::Entry; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::cmp::min` [INFO] [stdout] --> src/lib.rs:23:5 [INFO] [stdout] | [INFO] [stdout] 23 | use std::cmp::min; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections` [INFO] [stdout] --> src/lib.rs:24:5 [INFO] [stdout] | [INFO] [stdout] 24 | use std::collections; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `core::str::::trim_right`: superseded by `trim_end` [INFO] [stdout] --> src/lib.rs:201:14 [INFO] [stdout] | [INFO] [stdout] 201 | .trim_right() [INFO] [stdout] | ^^^^^^^^^^ help: replace the use of the deprecated associated function: `trim_end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `core::str::::trim_right`: superseded by `trim_end` [INFO] [stdout] --> src/lib.rs:207:14 [INFO] [stdout] | [INFO] [stdout] 207 | .trim_right() [INFO] [stdout] | ^^^^^^^^^^ help: replace the use of the deprecated associated function: `trim_end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `core::str::::trim_right`: superseded by `trim_end` [INFO] [stdout] --> src/lib.rs:201:14 [INFO] [stdout] | [INFO] [stdout] 201 | .trim_right() [INFO] [stdout] | ^^^^^^^^^^ help: replace the use of the deprecated associated function: `trim_end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `core::str::::trim_right`: superseded by `trim_end` [INFO] [stdout] --> src/lib.rs:207:14 [INFO] [stdout] | [INFO] [stdout] 207 | .trim_right() [INFO] [stdout] | ^^^^^^^^^^ help: replace the use of the deprecated associated function: `trim_end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `genome_of_contig` found for struct `genomes_and_contigs::GenomesAndContigs` in the current scope [INFO] [stdout] --> src/lib.rs:303:32 [INFO] [stdout] | [INFO] [stdout] 303 | *(contig_to_genome.genome_of_contig(&String::from("contig1")).unwrap())); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ method not found in `genomes_and_contigs::GenomesAndContigs` [INFO] [stdout] | [INFO] [stdout] ::: src/genomes_and_contigs.rs:8:1 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct GenomesAndContigs { [INFO] [stdout] | ---------------------------- method `genome_of_contig` not found for this [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `genome_of_contig` found for struct `genomes_and_contigs::GenomesAndContigs` in the current scope [INFO] [stdout] --> src/lib.rs:309:63 [INFO] [stdout] | [INFO] [stdout] 309 | assert_eq!(String::from("genome1"), *contig_to_genome.genome_of_contig(&String::from("seq1")).unwrap()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ method not found in `genomes_and_contigs::GenomesAndContigs` [INFO] [stdout] | [INFO] [stdout] ::: src/genomes_and_contigs.rs:8:1 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct GenomesAndContigs { [INFO] [stdout] | ---------------------------- method `genome_of_contig` not found for this [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/lib.rs:276:13 [INFO] [stdout] | [INFO] [stdout] 276 | let mut reader = Reader::from_file(path); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/lib.rs:277:13 [INFO] [stdout] | [INFO] [stdout] 277 | let mut name = file.to_string(); [INFO] [stdout] | ----^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `genome_of_contig` found for struct `genomes_and_contigs::GenomesAndContigs` in the current scope [INFO] [stdout] --> src/lib.rs:310:63 [INFO] [stdout] | [INFO] [stdout] 310 | assert_eq!(String::from("genome1"), *contig_to_genome.genome_of_contig(&String::from("seq2")).unwrap()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ method not found in `genomes_and_contigs::GenomesAndContigs` [INFO] [stdout] | [INFO] [stdout] ::: src/genomes_and_contigs.rs:8:1 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct GenomesAndContigs { [INFO] [stdout] | ---------------------------- method `genome_of_contig` not found for this [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/genomes_and_contigs.rs:40:17 [INFO] [stdout] | [INFO] [stdout] 40 | let mut gen = genome.lines(); [INFO] [stdout] | ----^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/genomes_and_contigs.rs:44:17 [INFO] [stdout] | [INFO] [stdout] 44 | let mut joined_genome = full_gen.join("").to_uppercase(); [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `find_first` [INFO] [stdout] --> src/genomes_and_contigs.rs:94:4 [INFO] [stdout] | [INFO] [stdout] 94 | fn find_first(slice: &[T], element: T) -> Result [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors; 7 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0599`. [INFO] [stdout] [INFO] [stderr] error: could not compile `kmer_indexer`. [INFO] [stdout] warning: 12 warnings emitted [INFO] [stdout] [INFO] [stdout] [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] error: build failed [INFO] running `Command { std: "docker" "inspect" "086d4c433b99b6819bb59dc9d3bc1a4993e08cebab878bbfab8e140af013f8ec", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "086d4c433b99b6819bb59dc9d3bc1a4993e08cebab878bbfab8e140af013f8ec", kill_on_drop: false }` [INFO] [stdout] 086d4c433b99b6819bb59dc9d3bc1a4993e08cebab878bbfab8e140af013f8ec