[INFO] cloning repository https://github.com/hillst/bamreadfilt [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/hillst/bamreadfilt" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fhillst%2Fbamreadfilt", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fhillst%2Fbamreadfilt'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] fbcf1d13b49dd648b7e51756c9b66987d9176b0c [INFO] checking hillst/bamreadfilt against try#c8bdaa84ec1b37f18f30375e196a65b7602f3790 for pr-73345 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fhillst%2Fbamreadfilt" "/workspace/builds/worker-9/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-9/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/hillst/bamreadfilt on toolchain c8bdaa84ec1b37f18f30375e196a65b7602f3790 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+c8bdaa84ec1b37f18f30375e196a65b7602f3790" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [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-9/source/Cargo.toml [INFO] crate git repo https://github.com/hillst/bamreadfilt already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+c8bdaa84ec1b37f18f30375e196a65b7602f3790" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] error: the lock file /workspace/builds/worker-9/source/Cargo.lock needs to be updated but --locked was passed to prevent this [INFO] [stderr] If you want to try to generate the lock file without accessing the network, use the --offline flag. [INFO] the lockfile is outdated, regenerating it [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+c8bdaa84ec1b37f18f30375e196a65b7602f3790" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }` [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+c8bdaa84ec1b37f18f30375e196a65b7602f3790" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded rust-htslib v0.16.0 [INFO] running `Command { std: "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_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env@sha256:6c9ffe128752d56c8d75334ed354142a5229917ed99767f56566dd8e857ad726" "/opt/rustwide/cargo-home/bin/cargo" "+c8bdaa84ec1b37f18f30375e196a65b7602f3790" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] 268d27b524339c682588740befe91355e98673f4d325e257bccb9e30bac4e3eb [INFO] running `Command { std: "docker" "start" "-a" "268d27b524339c682588740befe91355e98673f4d325e257bccb9e30bac4e3eb", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "268d27b524339c682588740befe91355e98673f4d325e257bccb9e30bac4e3eb", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "268d27b524339c682588740befe91355e98673f4d325e257bccb9e30bac4e3eb", kill_on_drop: false }` [INFO] [stdout] 268d27b524339c682588740befe91355e98673f4d325e257bccb9e30bac4e3eb [INFO] running `Command { std: "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=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@sha256:6c9ffe128752d56c8d75334ed354142a5229917ed99767f56566dd8e857ad726" "/opt/rustwide/cargo-home/bin/cargo" "+c8bdaa84ec1b37f18f30375e196a65b7602f3790" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 6fb665723502466ef91704cbb6a55972e3a4cac15fb35cca2f1b34fb829e600e [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" "6fb665723502466ef91704cbb6a55972e3a4cac15fb35cca2f1b34fb829e600e", kill_on_drop: false }` [INFO] [stderr] sudo: setrlimit(RLIMIT_CORE): Operation not permitted [INFO] [stderr] Compiling libc v0.2.71 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling memchr v2.3.3 [INFO] [stderr] Compiling log v0.4.8 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling cfg-if v0.1.10 [INFO] [stderr] Compiling libloading v0.4.3 [INFO] [stderr] Compiling ucd-util v0.1.8 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling utf8-ranges v1.0.4 [INFO] [stderr] Compiling unicode-width v0.1.7 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling bindgen v0.32.3 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling peeking_take_while v0.1.2 [INFO] [stderr] Checking tinyvec v0.3.3 [INFO] [stderr] Checking matches v0.1.8 [INFO] [stderr] Compiling byteorder v1.3.4 [INFO] [stderr] Checking either v1.5.3 [INFO] [stderr] Checking bitflags v0.9.1 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking argparse v0.2.2 [INFO] [stderr] Compiling proc-macro2 v0.2.3 [INFO] [stderr] Compiling clang-sys v0.21.2 [INFO] [stderr] Compiling thread_local v0.3.6 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling regex-syntax v0.5.6 [INFO] [stderr] Checking unicode-bidi v0.3.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking itertools v0.6.5 [INFO] [stderr] Checking unicode-normalization v0.1.13 [INFO] [stderr] Compiling log v0.3.9 [INFO] [stderr] Compiling quote v0.4.2 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling aho-corasick v0.6.10 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Compiling clap v2.33.1 [INFO] [stderr] Compiling nom v3.2.1 [INFO] [stderr] Checking idna v0.1.5 [INFO] [stderr] Checking url v1.7.2 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Compiling env_logger v0.4.3 [INFO] [stderr] Compiling rust-htslib v0.16.0 [INFO] [stderr] Checking bamreadfilt v0.1.1 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused imports: `StoreFalse`, `StoreOption` [INFO] [stdout] --> src/lib.rs:10:50 [INFO] [stdout] | [INFO] [stdout] 10 | use argparse::{ArgumentParser, StoreTrue, Store, StoreFalse, StoreOption}; [INFO] [stdout] | ^^^^^^^^^^ ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashSet` [INFO] [stdout] --> src/lib.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/lib.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `StoreFalse`, `StoreOption` [INFO] [stdout] --> src/lib.rs:10:50 [INFO] [stdout] | [INFO] [stdout] 10 | use argparse::{ArgumentParser, StoreTrue, Store, StoreFalse, StoreOption}; [INFO] [stdout] | ^^^^^^^^^^ ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashSet` [INFO] [stdout] --> src/lib.rs:11:5 [INFO] [stdout] | [INFO] [stdout] 11 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/lib.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fetched` [INFO] [stdout] --> src/lib.rs:218:13 [INFO] [stdout] | [INFO] [stdout] 218 | let fetched = match bam_reader.fetch(vcf_head.chrm, vcf_head.pos, vcf_head.pos + 1){ [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fetched` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fetched` [INFO] [stdout] --> src/lib.rs:242:21 [INFO] [stdout] | [INFO] [stdout] 242 | let fetched = match self._bam.fetch(rid, entry.pos(), entry.pos() + 1){ [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fetched` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `vcf` [INFO] [stdout] --> src/lib.rs:357:64 [INFO] [stdout] | [INFO] [stdout] 357 | pub fn collect_stats_stream(&mut self, item: &bam::Record, vcf: &VCFRecord, pir: usize) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_vcf` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fetched` [INFO] [stdout] --> src/lib.rs:218:13 [INFO] [stdout] | [INFO] [stdout] 218 | let fetched = match bam_reader.fetch(vcf_head.chrm, vcf_head.pos, vcf_head.pos + 1){ [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fetched` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fetched` [INFO] [stdout] --> src/lib.rs:242:21 [INFO] [stdout] | [INFO] [stdout] 242 | let fetched = match self._bam.fetch(rid, entry.pos(), entry.pos() + 1){ [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fetched` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `vcf` [INFO] [stdout] --> src/lib.rs:357:64 [INFO] [stdout] | [INFO] [stdout] 357 | pub fn collect_stats_stream(&mut self, item: &bam::Record, vcf: &VCFRecord, pir: usize) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_vcf` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant is never constructed: `BamRecord` [INFO] [stdout] --> src/lib.rs:437:5 [INFO] [stdout] | [INFO] [stdout] 437 | BamRecord(bam::Record), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `iter` [INFO] [stdout] --> src/lib.rs:485:8 [INFO] [stdout] | [INFO] [stdout] 485 | fn iter(&self) -> std::collections::hash_set::Iter { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `len` [INFO] [stdout] --> src/lib.rs:489:8 [INFO] [stdout] | [INFO] [stdout] 489 | fn len(&self) -> usize { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `max` [INFO] [stdout] --> src/lib.rs:493:8 [INFO] [stdout] | [INFO] [stdout] 493 | fn max(&self) -> Option<&UniqueRead> { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `min` [INFO] [stdout] --> src/lib.rs:497:8 [INFO] [stdout] | [INFO] [stdout] 497 | fn min(&self) -> Option<&UniqueRead> { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0635]: unknown feature `rand` [INFO] [stdout] --> src/lib.rs:2:12 [INFO] [stdout] | [INFO] [stdout] 2 | #![feature(rand)] [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ur_second` [INFO] [stdout] --> src/lib.rs:544:13 [INFO] [stdout] | [INFO] [stdout] 544 | let ur_second = UniqueRead { chrm: 1, pos: 1502, qname: "ayylmao_diff".to_string(), template_pos: true }; [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ur_second` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `i` [INFO] [stdout] --> src/lib.rs:601:13 [INFO] [stdout] | [INFO] [stdout] 601 | for i in 0..1000000 { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_i` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mean` [INFO] [stdout] --> src/lib.rs:617:14 [INFO] [stdout] | [INFO] [stdout] 617 | let (mean, var) = match ra.finalize(){ [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_mean` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `var` [INFO] [stdout] --> src/lib.rs:617:20 [INFO] [stdout] | [INFO] [stdout] 617 | let (mean, var) = match ra.finalize(){ [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_var` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `i` [INFO] [stdout] --> src/lib.rs:648:13 [INFO] [stdout] | [INFO] [stdout] 648 | for i in 0..1000000 { // 1 BILLION iterations [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_i` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `item` [INFO] [stdout] --> src/lib.rs:691:23 [INFO] [stdout] | [INFO] [stdout] 691 | Some((ref item, vcf, pir)) => { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_item` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `vcf` [INFO] [stdout] --> src/lib.rs:691:33 [INFO] [stdout] | [INFO] [stdout] 691 | Some((ref item, vcf, pir)) => { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_vcf` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bam` [INFO] [stdout] --> src/lib.rs:675:13 [INFO] [stdout] | [INFO] [stdout] 675 | let mut bam = bam::IndexedReader::from_path(path).ok().expect("Error opening bam."); [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bam` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to previous error; 11 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0635`. [INFO] [stdout] [INFO] [stderr] error: could not compile `bamreadfilt`. [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] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/lib.rs:616:13 [INFO] [stdout] | [INFO] [stdout] 616 | let mut ra = RunningAverage::new(); [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:675:13 [INFO] [stdout] | [INFO] [stdout] 675 | let mut bam = bam::IndexedReader::from_path(path).ok().expect("Error opening bam."); [INFO] [stdout] | ----^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant is never constructed: `BamRecord` [INFO] [stdout] --> src/lib.rs:437:5 [INFO] [stdout] | [INFO] [stdout] 437 | BamRecord(bam::Record), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `max` [INFO] [stdout] --> src/lib.rs:493:8 [INFO] [stdout] | [INFO] [stdout] 493 | fn max(&self) -> Option<&UniqueRead> { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `min` [INFO] [stdout] --> src/lib.rs:497:8 [INFO] [stdout] | [INFO] [stdout] 497 | fn min(&self) -> Option<&UniqueRead> { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0635]: unknown feature `rand` [INFO] [stdout] --> src/lib.rs:2:12 [INFO] [stdout] | [INFO] [stdout] 2 | #![feature(rand)] [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to previous error; 19 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0635`. [INFO] [stdout] [INFO] [stderr] error: build failed [INFO] running `Command { std: "docker" "inspect" "6fb665723502466ef91704cbb6a55972e3a4cac15fb35cca2f1b34fb829e600e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6fb665723502466ef91704cbb6a55972e3a4cac15fb35cca2f1b34fb829e600e", kill_on_drop: false }` [INFO] [stdout] 6fb665723502466ef91704cbb6a55972e3a4cac15fb35cca2f1b34fb829e600e