[INFO] cloning repository https://github.com/bluenote-1577/haplotype_phaser [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/bluenote-1577/haplotype_phaser" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] ec16ba688b0262f9b4d7fce917a5696872fc0153 [INFO] checking bluenote-1577/haplotype_phaser against master#a609fb45efad59dfd459c76e50899be9f0583b5a for pr-80579 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser" "/workspace/builds/worker-7/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-7/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/bluenote-1577/haplotype_phaser on toolchain a609fb45efad59dfd459c76e50899be9f0583b5a [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a609fb45efad59dfd459c76e50899be9f0583b5a" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/bluenote-1577/haplotype_phaser [INFO] finished tweaking git repo https://github.com/bluenote-1577/haplotype_phaser [INFO] tweaked toml for git repo https://github.com/bluenote-1577/haplotype_phaser written to /workspace/builds/worker-7/source/Cargo.toml [INFO] crate git repo https://github.com/bluenote-1577/haplotype_phaser already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a609fb45efad59dfd459c76e50899be9f0583b5a" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/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:b8eeb62f26c39b23691079a6cb6de528d8e88b4d71a8f6b1d30f8ba7d9c16de9" "/opt/rustwide/cargo-home/bin/cargo" "+a609fb45efad59dfd459c76e50899be9f0583b5a" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] eeb068440c646d39cd0a65b3da4c07f60b466ab0a565e17370a793239bdaeb42 [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" "eeb068440c646d39cd0a65b3da4c07f60b466ab0a565e17370a793239bdaeb42", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "eeb068440c646d39cd0a65b3da4c07f60b466ab0a565e17370a793239bdaeb42", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "eeb068440c646d39cd0a65b3da4c07f60b466ab0a565e17370a793239bdaeb42", kill_on_drop: false }` [INFO] [stdout] eeb068440c646d39cd0a65b3da4c07f60b466ab0a565e17370a793239bdaeb42 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/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:b8eeb62f26c39b23691079a6cb6de528d8e88b4d71a8f6b1d30f8ba7d9c16de9" "/opt/rustwide/cargo-home/bin/cargo" "+a609fb45efad59dfd459c76e50899be9f0583b5a" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 135bd9d96fe6577e7650d1d386688e56a9fe8a9f4a936f05261b66399b0cabd2 [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" "135bd9d96fe6577e7650d1d386688e56a9fe8a9f4a936f05261b66399b0cabd2", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.0.0 [INFO] [stderr] Compiling pkg-config v0.3.18 [INFO] [stderr] Checking cfg-if v0.1.10 [INFO] [stderr] Compiling proc-macro2 v1.0.19 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Compiling unicode-xid v0.2.1 [INFO] [stderr] Compiling syn v1.0.38 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling getrandom v0.1.14 [INFO] [stderr] Compiling memchr v2.3.3 [INFO] [stderr] Checking regex-syntax v0.6.18 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Checking ppv-lite86 v0.2.9 [INFO] [stderr] Compiling serde_derive v1.0.115 [INFO] [stderr] Checking tinyvec v0.3.4 [INFO] [stderr] Checking matches v0.1.8 [INFO] [stderr] Compiling rayon-core v1.7.1 [INFO] [stderr] Compiling serde v1.0.115 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Checking percent-encoding v2.1.0 [INFO] [stderr] Checking unicode-width v0.1.8 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking either v1.6.0 [INFO] [stderr] Checking ansi_term v0.11.0 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking strsim v0.8.0 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking predicates-core v1.0.0 [INFO] [stderr] Checking permute v0.1.0 [INFO] [stderr] Checking treeline v0.1.0 [INFO] [stderr] Checking difference v2.0.0 [INFO] [stderr] Checking normalize-line-endings v0.3.0 [INFO] [stderr] Compiling libc v0.2.74 [INFO] [stderr] Compiling libm v0.2.1 [INFO] [stderr] Compiling maybe-uninit v2.0.0 [INFO] [stderr] Compiling typenum v1.12.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking thread_local v1.0.1 [INFO] [stderr] Checking unicode-bidi v0.3.4 [INFO] [stderr] Compiling byteorder v1.3.4 [INFO] [stderr] Checking unicode-normalization v0.1.13 [INFO] [stderr] Checking matrixmultiply v0.2.3 [INFO] [stderr] Checking textwrap v0.11.0 [INFO] [stderr] Compiling doc-comment v0.3.3 [INFO] [stderr] Checking predicates-tree v1.0.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling standback v0.2.9 [INFO] [stderr] Compiling time v0.2.16 [INFO] [stderr] Compiling num-traits v0.2.12 [INFO] [stderr] Compiling crossbeam-utils v0.7.2 [INFO] [stderr] Compiling memoffset v0.5.5 [INFO] [stderr] Compiling crossbeam-epoch v0.8.2 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling num-integer v0.1.43 [INFO] [stderr] Compiling num-rational v0.2.4 [INFO] [stderr] Compiling rayon v1.3.1 [INFO] [stderr] Checking aho-corasick v0.7.13 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking idna v0.2.0 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Checking num_cpus v1.13.0 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking wait-timeout v0.2.0 [INFO] [stderr] Compiling quote v1.0.7 [INFO] [stderr] Checking clap v2.33.3 [INFO] [stderr] Checking rand_core v0.5.1 [INFO] [stderr] Compiling cc v1.0.59 [INFO] [stderr] Checking generic-array v0.13.2 [INFO] [stderr] Checking crossbeam-queue v0.2.3 [INFO] [stderr] Checking rand_chacha v0.2.2 [INFO] [stderr] Checking rand_pcg v0.2.1 [INFO] [stderr] Checking rand v0.7.3 [INFO] [stderr] Checking crossbeam-deque v0.7.3 [INFO] [stderr] Compiling openssl-src v111.10.2+1.1.1g [INFO] [stderr] Checking url v2.1.1 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking float-cmp v0.8.0 [INFO] [stderr] Compiling libz-sys v1.1.0 [INFO] [stderr] Compiling openssl-sys v0.9.58 [INFO] [stderr] Compiling curl-sys v0.4.36+curl-7.71.1 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.16 [INFO] [stderr] Compiling hts-sys v1.10.3 [INFO] [stderr] Checking regex v1.3.9 [INFO] [stderr] Checking alga v0.9.3 [INFO] [stderr] Checking rand_distr v0.2.2 [INFO] [stderr] Checking nalgebra v0.19.0 [INFO] [stderr] Checking predicates v1.0.5 [INFO] [stderr] Checking assert_cmd v1.0.1 [INFO] [stderr] Compiling thiserror-impl v1.0.20 [INFO] [stderr] Compiling time-macros-impl v0.1.1 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Checking time-macros v0.1.0 [INFO] [stderr] Checking thiserror v1.0.20 [INFO] [stderr] Checking bio-types v0.7.0 [INFO] [stderr] Checking statrs v0.13.0 [INFO] [stderr] Checking rust-htslib v0.32.0 [INFO] [stderr] Checking flopp v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: function is never used: `populate_clusters2_binom` [INFO] [stdout] --> src/local_clustering.rs:388:4 [INFO] [stdout] | [INFO] [stdout] 388 | fn populate_clusters2_binom( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `populate_clusters1` [INFO] [stdout] --> src/local_clustering.rs:489:4 [INFO] [stdout] | [INFO] [stdout] 489 | fn populate_clusters1( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `get_best_perms_mec` [INFO] [stdout] --> src/vcf_polishing.rs:118:4 [INFO] [stdout] | [INFO] [stdout] 118 | fn get_best_perms_mec(part1: &Vec>, part2: &Vec>) -> Vec> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `get_mec_from_part` [INFO] [stdout] --> src/vcf_polishing.rs:246:4 [INFO] [stdout] | [INFO] [stdout] 246 | fn get_mec_from_part(part : &Vec>) -> i32{ [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `populate_clusters2_binom` [INFO] [stdout] --> src/local_clustering.rs:388:4 [INFO] [stdout] | [INFO] [stdout] 388 | fn populate_clusters2_binom( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `populate_clusters1` [INFO] [stdout] --> src/local_clustering.rs:489:4 [INFO] [stdout] | [INFO] [stdout] 489 | fn populate_clusters1( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `get_best_perms_mec` [INFO] [stdout] --> src/vcf_polishing.rs:118:4 [INFO] [stdout] | [INFO] [stdout] 118 | fn get_best_perms_mec(part1: &Vec>, part2: &Vec>) -> Vec> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `get_mec_from_part` [INFO] [stdout] --> src/vcf_polishing.rs:246:4 [INFO] [stdout] | [INFO] [stdout] 246 | fn get_mec_from_part(part : &Vec>) -> i32{ [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `predicates::prelude::*` [INFO] [stdout] --> tests/integration_test.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use predicates::prelude::*; // Used for writing assertions [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `FxHashMap` [INFO] [stdout] --> tests/frag_reader_test.rs:5:24 [INFO] [stdout] | [INFO] [stdout] 5 | use fxhash::{FxHashSet,FxHashMap}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashSet` [INFO] [stdout] --> tests/frag_reader_test.rs:6:24 [INFO] [stdout] | [INFO] [stdout] 6 | use std::collections::{HashSet,BTreeMap}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unnecessary trailing semicolon [INFO] [stdout] --> tests/frag_reader_test.rs:80:48 [INFO] [stdout] | [INFO] [stdout] 80 | let mut hashset_int = FxHashSet::default();; [INFO] [stdout] | ^ help: remove this semicolon [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(redundant_semicolons)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `indexed_reads` [INFO] [stdout] --> tests/frag_reader_test.rs:47:9 [INFO] [stdout] | [INFO] [stdout] 47 | let indexed_reads = utils_frags::get_all_overlaps(&frags); [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_indexed_reads` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [optimized + debuginfo] target(s) in 4m 01s [INFO] running `Command { std: "docker" "inspect" "135bd9d96fe6577e7650d1d386688e56a9fe8a9f4a936f05261b66399b0cabd2", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "135bd9d96fe6577e7650d1d386688e56a9fe8a9f4a936f05261b66399b0cabd2", kill_on_drop: false }` [INFO] [stdout] 135bd9d96fe6577e7650d1d386688e56a9fe8a9f4a936f05261b66399b0cabd2