[INFO] updating cached repository https://github.com/wheaton5/long_read_binner [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] e72d4e667fc1c4e41b1616f1924744f0d4e76bd7 [INFO] checking wheaton5/long_read_binner against try#ea663bba38739867a4b75ac820991b4f5d093c3b for pr-62262-1 [INFO] running `"git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Flong_read_binner" "/workspace/builds/worker-2/source"` [INFO] [stderr] Cloning into '/workspace/builds/worker-2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/wheaton5/long_read_binner on toolchain ea663bba38739867a4b75ac820991b4f5d093c3b [INFO] running `"/workspace/cargo-home/bin/cargo" "+ea663bba38739867a4b75ac820991b4f5d093c3b" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] started tweaking git repo https://github.com/wheaton5/long_read_binner [INFO] finished tweaking git repo https://github.com/wheaton5/long_read_binner [INFO] tweaked toml for git repo https://github.com/wheaton5/long_read_binner written to /workspace/builds/worker-2/source/Cargo.toml [INFO] crate git repo https://github.com/wheaton5/long_read_binner already has a lockfile, it will not be regenerated [INFO] running `"/workspace/cargo-home/bin/cargo" "+ea663bba38739867a4b75ac820991b4f5d093c3b" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Updating git repository `https://github.com/wheaton5/dna_io.git` [INFO] [stderr] error: the lock file /workspace/builds/worker-2/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needs to be updated but --locked was passed to prevent this [INFO] the lockfile is outdated, regenerating it [INFO] running `"/workspace/cargo-home/bin/cargo" "+ea663bba38739867a4b75ac820991b4f5d093c3b" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] [stderr] Updating git repository `https://github.com/10XGenomics/rust-debruijn.git` [INFO] [stderr] Updating git repository `https://github.com/wheaton5/dna_io.git` [INFO] running `"/workspace/cargo-home/bin/cargo" "+ea663bba38739867a4b75ac820991b4f5d093c3b" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2/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" "+ea663bba38739867a4b75ac820991b4f5d093c3b" "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] 946565af06ff1bb3b794e19ccd993a6ecd40a27e7cb51661a77d09234b66c7fc [INFO] running `"docker" "start" "-a" "946565af06ff1bb3b794e19ccd993a6ecd40a27e7cb51661a77d09234b66c7fc"` [INFO] [stderr] Compiling log v0.4.8 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling serde v1.0.101 [INFO] [stderr] Compiling regex-syntax v0.6.12 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling yaml-rust v0.3.5 [INFO] [stderr] Compiling bindgen v0.51.1 [INFO] [stderr] Compiling strsim v0.6.0 [INFO] [stderr] Compiling ansi_term v0.9.0 [INFO] [stderr] Compiling shlex v0.1.1 [INFO] [stderr] Compiling doc-comment v0.3.1 [INFO] [stderr] Compiling ryu v1.0.2 [INFO] [stderr] Checking spin v0.4.10 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Compiling proc-macro2 v1.0.6 [INFO] [stderr] Compiling num-traits v0.2.8 [INFO] [stderr] Compiling num-integer v0.1.41 [INFO] [stderr] Compiling backtrace-sys v0.1.32 [INFO] [stderr] Compiling num-bigint v0.2.3 [INFO] [stderr] Checking thread_local v0.3.6 [INFO] [stderr] Compiling num-rational v0.2.2 [INFO] [stderr] Compiling num-iter v0.1.39 [INFO] [stderr] Compiling num-complex v0.2.3 [INFO] [stderr] Compiling nom v4.2.3 [INFO] [stderr] Compiling clang-sys v0.28.1 [INFO] [stderr] Compiling lzma-sys v0.1.15 [INFO] [stderr] Compiling arrayvec v0.4.12 [INFO] [stderr] Compiling humantime v1.3.0 [INFO] [stderr] Compiling fs-utils v1.1.1 [INFO] [stderr] Compiling textwrap v0.9.0 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking wyhash v0.3.0 [INFO] [stderr] Compiling rayon-core v1.6.0 [INFO] [stderr] Checking miniz_oxide v0.3.3 [INFO] [stderr] Checking concurrent-hashmap v0.2.2 [INFO] [stderr] Compiling libloading v0.5.2 [INFO] [stderr] Checking crossbeam-queue v0.1.2 [INFO] [stderr] Compiling byteorder v1.3.2 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Checking idna v0.2.0 [INFO] [stderr] Checking crc32fast v1.2.0 [INFO] [stderr] Checking rand v0.5.6 [INFO] [stderr] Compiling atty v0.2.13 [INFO] [stderr] Compiling which v3.0.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling quote v1.0.2 [INFO] [stderr] Compiling rustc-hash v1.0.1 [INFO] [stderr] Checking clap v2.27.1 [INFO] [stderr] Checking flate2 v1.0.12 [INFO] [stderr] Compiling regex v1.3.1 [INFO] [stderr] Checking url v2.1.0 [INFO] [stderr] Checking backtrace v0.3.40 [INFO] [stderr] Compiling syn v1.0.5 [INFO] [stderr] Compiling cexpr v0.3.5 [INFO] [stderr] Compiling env_logger v0.6.2 [INFO] [stderr] Checking crossbeam-epoch v0.7.2 [INFO] [stderr] Checking crossbeam-deque v0.7.1 [INFO] [stderr] Checking rayon v1.2.0 [INFO] [stderr] Checking num v0.2.0 [INFO] [stderr] Compiling serde_derive v1.0.101 [INFO] [stderr] Compiling snafu-derive v0.5.0 [INFO] [stderr] Checking snafu v0.5.0 [INFO] [stderr] Compiling rust-htslib v0.26.0 [INFO] [stderr] Checking bio-types v0.5.1 [INFO] [stderr] Checking serde_json v1.0.41 [INFO] [stderr] Checking boomphf v0.5.2 [INFO] [stderr] Checking debruijn v0.3.0 (https://github.com/10XGenomics/rust-debruijn.git#b3d5db74) [INFO] [stderr] Checking dna_io v0.1.0 (https://github.com/wheaton5/dna_io.git#a640f47b) [INFO] [stderr] error[E0432]: unresolved import `rust_htslib::sam` [INFO] [stderr] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:15:5 [INFO] [stderr] | [INFO] [stderr] 15 | use rust_htslib::sam; [INFO] [stderr] | ^^^^^^^^^^^^^--- [INFO] [stderr] | | | [INFO] [stderr] | | help: a similar name exists in the module: `bam` [INFO] [stderr] | no `sam` in the root [INFO] [stderr] [INFO] [stderr] error[E0432]: unresolved imports `rust_htslib::prelude`, `DnaReader`, `DnaRecord`, `DnaWriter`, `DnaWrite`, `flush` [INFO] [stderr] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:17:18 [INFO] [stderr] | [INFO] [stderr] 17 | use rust_htslib::prelude::*; [INFO] [stderr] | ^^^^^^^ could not find `prelude` in `rust_htslib` [INFO] [stderr] ... [INFO] [stderr] 442 | use DnaReader; [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] 443 | #[allow(unused_imports)] [INFO] [stderr] 444 | use DnaRecord; [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] 445 | #[allow(unused_imports)] [INFO] [stderr] 446 | use DnaWriter; [INFO] [stderr] | ^^^^^^^^^ [INFO] [stderr] 447 | use DnaWrite; [INFO] [stderr] | ^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 450 | use flush; [INFO] [stderr] | ^^^^^ [INFO] [stderr] [INFO] [stderr] error[E0433]: failed to resolve: could not find `ReadError` in `bam` [INFO] [stderr] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:360:22 [INFO] [stderr] | [INFO] [stderr] 360 | Err(bam::ReadError::NoMoreRecord) => return None, [INFO] [stderr] | ^^^^^^^^^ could not find `ReadError` in `bam` [INFO] [stderr] [INFO] [stderr] error[E0599]: no method named `header` found for type `rust_htslib::bam::Reader` in the current scope [INFO] [stderr] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:350:52 [INFO] [stderr] | [INFO] [stderr] 350 | let header = bam::Header::from_template(template.header()); [INFO] [stderr] | ^^^^^^ private field, not a method [INFO] [stderr] | [INFO] [stderr] = help: items from traits can only be used if the trait is in scope [INFO] [stderr] help: the following trait is implemented but not in scope; perhaps add a `use` for it: [INFO] [stderr] | [INFO] [stderr] 4 | use rust_htslib::bam::Read; [INFO] [stderr] | [INFO] [stderr] [INFO] [stderr] error[E0061]: this function takes 3 parameters but 2 parameters were supplied [INFO] [stderr] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:351:17 [INFO] [stderr] | [INFO] [stderr] 351 | let mut bam = bam::Writer::from_path(filename, &header).expect("could not open bam for writing"); [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected 3 parameters [INFO] [stderr] [INFO] [stderr] error[E0599]: no method named `read` found for type `rust_htslib::bam::Reader` in the current scope [INFO] [stderr] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:359:21 [INFO] [stderr] | [INFO] [stderr] 359 | match self.reader.read(&mut record) { [INFO] [stderr] | ^^^^ method not found in `rust_htslib::bam::Reader` [INFO] [stderr] | [INFO] [stderr] = help: items from traits can only be used if the trait is in scope [INFO] [stderr] help: the following trait is implemented but not in scope; perhaps add a `use` for it: [INFO] [stderr] | [INFO] [stderr] 4 | use rust_htslib::bam::Read; [INFO] [stderr] | [INFO] [stderr] [INFO] [stderr] error[E0599]: no method named `header` found for type `rust_htslib::bam::Reader` in the current scope [INFO] [stderr] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:372:91 [INFO] [stderr] | [INFO] [stderr] 372 | fn header(&self) -> Option { Some(bam::Header::from_template(self.reader.header())) } [INFO] [stderr] | ^^^^^^ private field, not a method [INFO] [stderr] | [INFO] [stderr] = help: items from traits can only be used if the trait is in scope [INFO] [stderr] help: the following trait is implemented but not in scope; perhaps add a `use` for it: [INFO] [stderr] | [INFO] [stderr] 4 | use rust_htslib::bam::Read; [INFO] [stderr] | [INFO] [stderr] [INFO] [stderr] error: aborting due to 7 previous errors [INFO] [stderr] [INFO] [stderr] Some errors have detailed explanations: E0061, E0432, E0433, E0599. [INFO] [stderr] For more information about an error, try `rustc --explain E0061`. [INFO] [stderr] error: could not compile `dna_io`. [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [INFO] running `"docker" "inspect" "946565af06ff1bb3b794e19ccd993a6ecd40a27e7cb51661a77d09234b66c7fc"` [INFO] running `"docker" "rm" "-f" "946565af06ff1bb3b794e19ccd993a6ecd40a27e7cb51661a77d09234b66c7fc"` [INFO] [stdout] 946565af06ff1bb3b794e19ccd993a6ecd40a27e7cb51661a77d09234b66c7fc