[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] 451c40cb7beb3c32eb64c42ed165b16126358e7d [INFO] checking hillst/bamreadfilt against master#1557fb031b272b4c5bfcc7de5df7eddc7b36a584 for pr-73166 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fhillst%2Fbamreadfilt" "/workspace/builds/worker-5/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-5/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/hillst/bamreadfilt on toolchain 1557fb031b272b4c5bfcc7de5df7eddc7b36a584 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1557fb031b272b4c5bfcc7de5df7eddc7b36a584" "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-5/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" "+1557fb031b272b4c5bfcc7de5df7eddc7b36a584" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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:a636fd89d022f18117e1dc8fb37a0a009933cdbbe082814857f0e2024962d47c" "/opt/rustwide/cargo-home/bin/cargo" "+1557fb031b272b4c5bfcc7de5df7eddc7b36a584" "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] 537e5c80cd75a3ee9c45f4a2e82cfba86bcc0eb8e4eff887b0e8d3cfba685a6f [INFO] running `Command { std: "docker" "start" "-a" "537e5c80cd75a3ee9c45f4a2e82cfba86bcc0eb8e4eff887b0e8d3cfba685a6f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "537e5c80cd75a3ee9c45f4a2e82cfba86bcc0eb8e4eff887b0e8d3cfba685a6f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "537e5c80cd75a3ee9c45f4a2e82cfba86bcc0eb8e4eff887b0e8d3cfba685a6f", kill_on_drop: false }` [INFO] [stdout] 537e5c80cd75a3ee9c45f4a2e82cfba86bcc0eb8e4eff887b0e8d3cfba685a6f [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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:a636fd89d022f18117e1dc8fb37a0a009933cdbbe082814857f0e2024962d47c" "/opt/rustwide/cargo-home/bin/cargo" "+1557fb031b272b4c5bfcc7de5df7eddc7b36a584" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 85226d9bee271c2aa4587ad4df12fdd74013200965f683856d5310d9112cac41 [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" "85226d9bee271c2aa4587ad4df12fdd74013200965f683856d5310d9112cac41", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.71 [INFO] [stderr] Compiling glob v0.2.11 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling libloading v0.4.3 [INFO] [stderr] Compiling cfg-if v0.1.10 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling unicode-width v0.1.8 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling bindgen v0.32.3 [INFO] [stderr] Compiling vec_map v0.8.2 [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] Compiling byteorder v1.3.4 [INFO] [stderr] Checking either v1.5.3 [INFO] [stderr] Checking percent-encoding v1.0.1 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking bitflags v0.9.1 [INFO] [stderr] Checking lazy_static v0.2.11 [INFO] [stderr] Checking argparse v0.2.2 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling proc-macro2 v0.2.3 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Checking itertools v0.6.5 [INFO] [stderr] Compiling memchr v2.3.3 [INFO] [stderr] Compiling log v0.4.8 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling log v0.3.9 [INFO] [stderr] Checking unicode-normalization v0.1.13 [INFO] [stderr] Compiling clang-sys v0.21.2 [INFO] [stderr] Compiling aho-corasick v0.6.10 [INFO] [stderr] Compiling quote v0.4.2 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Compiling clap v2.33.1 [INFO] [stderr] Compiling nom v3.2.1 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Checking idna v0.1.5 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Checking url v1.7.2 [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] error[E0432]: unresolved import `test` [INFO] [stdout] --> src/lib.rs:519:9 [INFO] [stdout] | [INFO] [stdout] 519 | use test::Bencher; [INFO] [stdout] | ^^^^ [INFO] [stdout] | | [INFO] [stdout] | unresolved import [INFO] [stdout] | help: a similar path exists: `tests::test::test` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `StoreFalse`, `StoreOption` [INFO] [stdout] --> src/lib.rs:5:50 [INFO] [stdout] | [INFO] [stdout] 5 | 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:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/lib.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: use of unstable library feature 'test': `bench` is a part of custom test frameworks which are unstable [INFO] [stdout] --> src/lib.rs:658:7 [INFO] [stdout] | [INFO] [stdout] 658 | #[bench] [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[deny(soft_unstable)]` on by default [INFO] [stdout] = warning: this was previously accepted by the compiler but is being phased out; it will become a hard error in a future release! [INFO] [stdout] = note: for more information, see issue #64266 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `StoreFalse`, `StoreOption` [INFO] [stdout] --> src/lib.rs:5:50 [INFO] [stdout] | [INFO] [stdout] 5 | 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:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use std::collections::HashSet; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/lib.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fetched` [INFO] [stdout] --> src/lib.rs:213:13 [INFO] [stdout] | [INFO] [stdout] 213 | 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:237:21 [INFO] [stdout] | [INFO] [stdout] 237 | 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:352:64 [INFO] [stdout] | [INFO] [stdout] 352 | 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] error[E0308]: mismatched types [INFO] [stdout] --> src/lib.rs:595:23 [INFO] [stdout] | [INFO] [stdout] 595 | ra.update(i); [INFO] [stdout] | ^ expected `f64`, found integer [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors; 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0308, E0432. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0308`. [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: variant is never constructed: `BamRecord` [INFO] [stdout] --> src/lib.rs:432:5 [INFO] [stdout] | [INFO] [stdout] 432 | 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:480:8 [INFO] [stdout] | [INFO] [stdout] 480 | 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:484:8 [INFO] [stdout] | [INFO] [stdout] 484 | fn len(&self) -> usize { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function is never used: `max` [INFO] [stdout] --> src/lib.rs:488:8 [INFO] [stdout] | [INFO] [stdout] 488 | 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:492:8 [INFO] [stdout] | [INFO] [stdout] 492 | fn min(&self) -> Option<&UniqueRead> { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 11 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: build failed [INFO] running `Command { std: "docker" "inspect" "85226d9bee271c2aa4587ad4df12fdd74013200965f683856d5310d9112cac41", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "85226d9bee271c2aa4587ad4df12fdd74013200965f683856d5310d9112cac41", kill_on_drop: false }` [INFO] [stdout] 85226d9bee271c2aa4587ad4df12fdd74013200965f683856d5310d9112cac41