[INFO] updating cached repository https://github.com/hillst/bamreadfilt [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] fbcf1d13b49dd648b7e51756c9b66987d9176b0c [INFO] checking hillst/bamreadfilt against master#b61e69433951e31f7bd746e22f516a48ad41623b for prs-64470-and-65389 [INFO] running `"git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fhillst%2Fbamreadfilt" "/workspace/builds/worker-4/source"` [INFO] [stderr] Cloning into '/workspace/builds/worker-4/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/hillst/bamreadfilt on toolchain b61e69433951e31f7bd746e22f516a48ad41623b [INFO] running `"/workspace/cargo-home/bin/cargo" "+b61e69433951e31f7bd746e22f516a48ad41623b" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] started tweaking git repo https://github.com/hillst/bamreadfilt [INFO] finished tweaking git repo https://github.com/hillst/bamreadfilt [INFO] tweaked toml for git repo https://github.com/hillst/bamreadfilt written to /workspace/builds/worker-4/source/Cargo.toml [INFO] crate git repo https://github.com/hillst/bamreadfilt already has a lockfile, it will not be regenerated [INFO] running `"/workspace/cargo-home/bin/cargo" "+b61e69433951e31f7bd746e22f516a48ad41623b" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Updating crates.io index [INFO] [stderr] error: the lock file /workspace/builds/worker-4/source/Cargo.lock needs to be updated but --locked was passed to prevent this [INFO] the lockfile is outdated, regenerating it [INFO] running `"/workspace/cargo-home/bin/cargo" "+b61e69433951e31f7bd746e22f516a48ad41623b" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/workspace/cargo-home/bin/cargo" "+b61e69433951e31f7bd746e22f516a48ad41623b" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/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" "+b61e69433951e31f7bd746e22f516a48ad41623b" "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] 735c5abf4a9c4f879cd4757115f80dd2c5bf355e599e9eb28c5f3d8c6871780e [INFO] running `"docker" "start" "-a" "735c5abf4a9c4f879cd4757115f80dd2c5bf355e599e9eb28c5f3d8c6871780e"` [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Compiling fs-utils v1.1.1 [INFO] [stderr] Compiling rust-htslib v0.16.0 [INFO] [stderr] Checking bamreadfilt v0.1.1 (/opt/rustwide/workdir) [INFO] [stderr] warning: unused imports: `StoreFalse`, `StoreOption` [INFO] [stderr] --> src/lib.rs:10:50 [INFO] [stderr] | [INFO] [stderr] 10 | use argparse::{ArgumentParser, StoreTrue, Store, StoreFalse, StoreOption}; [INFO] [stderr] | ^^^^^^^^^^ ^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::collections::HashSet` [INFO] [stderr] --> src/lib.rs:11:5 [INFO] [stderr] | [INFO] [stderr] 11 | use std::collections::HashSet; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::fs::File` [INFO] [stderr] --> src/lib.rs:15:5 [INFO] [stderr] | [INFO] [stderr] 15 | use std::fs::File; [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused variable: `fetched` [INFO] [stderr] --> src/lib.rs:218:13 [INFO] [stderr] | [INFO] [stderr] 218 | let fetched = match bam_reader.fetch(vcf_head.chrm, vcf_head.pos, vcf_head.pos + 1){ [INFO] [stderr] | ^^^^^^^ help: consider prefixing with an underscore: `_fetched` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `fetched` [INFO] [stderr] --> src/lib.rs:242:21 [INFO] [stderr] | [INFO] [stderr] 242 | let fetched = match self._bam.fetch(rid, entry.pos(), entry.pos() + 1){ [INFO] [stderr] | ^^^^^^^ help: consider prefixing with an underscore: `_fetched` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `vcf` [INFO] [stderr] --> src/lib.rs:357:64 [INFO] [stderr] | [INFO] [stderr] 357 | pub fn collect_stats_stream(&mut self, item: &bam::Record, vcf: &VCFRecord, pir: usize) { [INFO] [stderr] | ^^^ help: consider prefixing with an underscore: `_vcf` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `ur_second` [INFO] [stderr] --> src/lib.rs:544:13 [INFO] [stderr] | [INFO] [stderr] 544 | let ur_second = UniqueRead { chrm: 1, pos: 1502, qname: "ayylmao_diff".to_string(), template_pos: true }; [INFO] [stderr] | ^^^^^^^^^ help: consider prefixing with an underscore: `_ur_second` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `i` [INFO] [stderr] --> src/lib.rs:601:13 [INFO] [stderr] | [INFO] [stderr] 601 | for i in 0..1000000 { [INFO] [stderr] | ^ help: consider prefixing with an underscore: `_i` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `mean` [INFO] [stderr] --> src/lib.rs:617:14 [INFO] [stderr] | [INFO] [stderr] 617 | let (mean, var) = match ra.finalize(){ [INFO] [stderr] | ^^^^ help: consider prefixing with an underscore: `_mean` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `var` [INFO] [stderr] --> src/lib.rs:617:20 [INFO] [stderr] | [INFO] [stderr] 617 | let (mean, var) = match ra.finalize(){ [INFO] [stderr] | ^^^ help: consider prefixing with an underscore: `_var` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `i` [INFO] [stderr] --> src/lib.rs:648:13 [INFO] [stderr] | [INFO] [stderr] 648 | for i in 0..1000000 { // 1 BILLION iterations [INFO] [stderr] | ^ help: consider prefixing with an underscore: `_i` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `item` [INFO] [stderr] --> src/lib.rs:691:27 [INFO] [stderr] | [INFO] [stderr] 691 | Some((ref item, vcf, pir)) => { [INFO] [stderr] | ^^^^ help: consider prefixing with an underscore: `_item` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `vcf` [INFO] [stderr] --> src/lib.rs:691:33 [INFO] [stderr] | [INFO] [stderr] 691 | Some((ref item, vcf, pir)) => { [INFO] [stderr] | ^^^ help: consider prefixing with an underscore: `_vcf` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `bam` [INFO] [stderr] --> src/lib.rs:675:17 [INFO] [stderr] | [INFO] [stderr] 675 | let mut bam = bam::IndexedReader::from_path(path).ok().expect("Error opening bam."); [INFO] [stderr] | ^^^ help: consider prefixing with an underscore: `_bam` [INFO] [stderr] [INFO] [stderr] warning: variable does not need to be mutable [INFO] [stderr] --> src/lib.rs:616:13 [INFO] [stderr] | [INFO] [stderr] 616 | let mut ra = RunningAverage::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/lib.rs:675:13 [INFO] [stderr] | [INFO] [stderr] 675 | let mut bam = bam::IndexedReader::from_path(path).ok().expect("Error opening bam."); [INFO] [stderr] | ----^^^ [INFO] [stderr] | | [INFO] [stderr] | help: remove this `mut` [INFO] [stderr] [INFO] [stderr] warning: variant is never constructed: `BamRecord` [INFO] [stderr] --> src/lib.rs:437:5 [INFO] [stderr] | [INFO] [stderr] 437 | BamRecord(bam::Record), [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: method is never used: `max` [INFO] [stderr] --> src/lib.rs:493:5 [INFO] [stderr] | [INFO] [stderr] 493 | fn max(&self) -> Option<&UniqueRead> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: method is never used: `min` [INFO] [stderr] --> src/lib.rs:497:5 [INFO] [stderr] | [INFO] [stderr] 497 | fn min(&self) -> Option<&UniqueRead> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] error[E0635]: unknown feature `rand` [INFO] [stderr] --> src/lib.rs:2:12 [INFO] [stderr] | [INFO] [stderr] 2 | #![feature(rand)] [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] error: aborting due to previous error [INFO] [stderr] [INFO] [stderr] For more information about this error, try `rustc --explain E0635`. [INFO] [stderr] warning: unused imports: `StoreFalse`, `StoreOption` [INFO] [stderr] --> src/lib.rs:10:50 [INFO] [stderr] | [INFO] [stderr] 10 | use argparse::{ArgumentParser, StoreTrue, Store, StoreFalse, StoreOption}; [INFO] [stderr] | ^^^^^^^^^^ ^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::collections::HashSet` [INFO] [stderr] --> src/lib.rs:11:5 [INFO] [stderr] | [INFO] [stderr] 11 | use std::collections::HashSet; [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: unused import: `std::fs::File` [INFO] [stderr] --> src/lib.rs:15:5 [INFO] [stderr] | [INFO] [stderr] 15 | use std::fs::File; [INFO] [stderr] | ^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] error: could not compile `bamreadfilt`. [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stderr] warning: unused variable: `fetched` [INFO] [stderr] --> src/lib.rs:218:13 [INFO] [stderr] | [INFO] [stderr] 218 | let fetched = match bam_reader.fetch(vcf_head.chrm, vcf_head.pos, vcf_head.pos + 1){ [INFO] [stderr] | ^^^^^^^ help: consider prefixing with an underscore: `_fetched` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `fetched` [INFO] [stderr] --> src/lib.rs:242:21 [INFO] [stderr] | [INFO] [stderr] 242 | let fetched = match self._bam.fetch(rid, entry.pos(), entry.pos() + 1){ [INFO] [stderr] | ^^^^^^^ help: consider prefixing with an underscore: `_fetched` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `vcf` [INFO] [stderr] --> src/lib.rs:357:64 [INFO] [stderr] | [INFO] [stderr] 357 | pub fn collect_stats_stream(&mut self, item: &bam::Record, vcf: &VCFRecord, pir: usize) { [INFO] [stderr] | ^^^ help: consider prefixing with an underscore: `_vcf` [INFO] [stderr] [INFO] [stderr] warning: variant is never constructed: `BamRecord` [INFO] [stderr] --> src/lib.rs:437:5 [INFO] [stderr] | [INFO] [stderr] 437 | BamRecord(bam::Record), [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: method is never used: `iter` [INFO] [stderr] --> src/lib.rs:485:5 [INFO] [stderr] | [INFO] [stderr] 485 | fn iter(&self) -> std::collections::hash_set::Iter { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: method is never used: `len` [INFO] [stderr] --> src/lib.rs:489:5 [INFO] [stderr] | [INFO] [stderr] 489 | fn len(&self) -> usize { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: method is never used: `max` [INFO] [stderr] --> src/lib.rs:493:5 [INFO] [stderr] | [INFO] [stderr] 493 | fn max(&self) -> Option<&UniqueRead> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: method is never used: `min` [INFO] [stderr] --> src/lib.rs:497:5 [INFO] [stderr] | [INFO] [stderr] 497 | fn min(&self) -> Option<&UniqueRead> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] error[E0635]: unknown feature `rand` [INFO] [stderr] --> src/lib.rs:2:12 [INFO] [stderr] | [INFO] [stderr] 2 | #![feature(rand)] [INFO] [stderr] | ^^^^ [INFO] [stderr] [INFO] [stderr] error: aborting due to previous error [INFO] [stderr] [INFO] [stderr] For more information about this error, try `rustc --explain E0635`. [INFO] [stderr] error: could not compile `bamreadfilt`. [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [INFO] running `"docker" "inspect" "735c5abf4a9c4f879cd4757115f80dd2c5bf355e599e9eb28c5f3d8c6871780e"` [INFO] running `"docker" "rm" "-f" "735c5abf4a9c4f879cd4757115f80dd2c5bf355e599e9eb28c5f3d8c6871780e"` [INFO] [stdout] 735c5abf4a9c4f879cd4757115f80dd2c5bf355e599e9eb28c5f3d8c6871780e