[INFO] updating cached repository https://github.com/wheaton5/distinguishing_kmers [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] 956d14d256c7fea54b7e8b072fc67bc99e98e594 [INFO] testing wheaton5/distinguishing_kmers against beta-2020-06-03 for beta-1.45-1 [INFO] running `"git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Fdistinguishing_kmers" "/workspace/builds/worker-11/source"` [INFO] [stderr] Cloning into '/workspace/builds/worker-11/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/wheaton5/distinguishing_kmers on toolchain beta-2020-06-03 [INFO] running `"/workspace/cargo-home/bin/cargo" "+beta-2020-06-03" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] started tweaking git repo https://github.com/wheaton5/distinguishing_kmers [INFO] finished tweaking git repo https://github.com/wheaton5/distinguishing_kmers [INFO] tweaked toml for git repo https://github.com/wheaton5/distinguishing_kmers written to /workspace/builds/worker-11/source/Cargo.toml [INFO] crate git repo https://github.com/wheaton5/distinguishing_kmers already has a lockfile, it will not be regenerated [INFO] running `"/workspace/cargo-home/bin/cargo" "+beta-2020-06-03" "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-11/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 [INFO] the lockfile is outdated, regenerating it [INFO] running `"/workspace/cargo-home/bin/cargo" "+beta-2020-06-03" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] [stderr] Blocking waiting for file lock on package cache [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" "+beta-2020-06-03" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/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=warn" "-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" "+beta-2020-06-03" "build" "--frozen"` [INFO] [stdout] d2b838b1db42e3473c4c080f10b717781b55ab0bc395391239aaa3ee014ab05a [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `"docker" "start" "-a" "d2b838b1db42e3473c4c080f10b717781b55ab0bc395391239aaa3ee014ab05a"` [INFO] [stderr] sudo: setrlimit(RLIMIT_CORE): Operation not permitted [INFO] [stderr] Compiling syn v1.0.30 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling regex-syntax v0.6.18 [INFO] [stderr] Compiling bindgen v0.53.3 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling shlex v0.1.1 [INFO] [stderr] Compiling peeking_take_while v0.1.2 [INFO] [stderr] Compiling doc-comment v0.3.3 [INFO] [stderr] Compiling rand_core v0.4.2 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling itoa v0.4.5 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling bit-vec v0.6.2 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling yaml-rust v0.3.5 [INFO] [stderr] Compiling bit-vec v0.4.4 [INFO] [stderr] Compiling num-traits v0.2.11 [INFO] [stderr] Compiling num-bigint v0.2.6 [INFO] [stderr] Compiling num-rational v0.2.4 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling num-iter v0.1.40 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.16 [INFO] [stderr] Compiling curl-sys v0.4.31+curl-7.70.0 [INFO] [stderr] Compiling itertools v0.8.2 [INFO] [stderr] Compiling nom v5.1.1 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling miniz_oxide v0.3.6 [INFO] [stderr] Compiling textwrap v0.9.0 [INFO] [stderr] Compiling wyhash v0.3.0 [INFO] [stderr] Compiling bloom v0.3.2 [INFO] [stderr] Compiling bit-set v0.5.2 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling clap v2.27.1 [INFO] [stderr] Compiling clang-sys v0.29.3 [INFO] [stderr] Compiling flate2 v1.0.14 [INFO] [stderr] Compiling num-integer v0.1.42 [INFO] [stderr] Compiling regex v1.3.9 [INFO] [stderr] Compiling cexpr v0.4.0 [INFO] [stderr] Compiling num v0.2.1 [INFO] [stderr] Compiling serde_derive v1.0.111 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling snafu-derive v0.6.8 [INFO] [stderr] Compiling snafu v0.6.0 [INFO] [stderr] Compiling hts-sys v1.10.2 [INFO] [stderr] Compiling serde v1.0.111 [INFO] [stderr] Compiling bio-types v0.6.0 [INFO] [stderr] Compiling serde_json v1.0.53 [INFO] [stderr] Compiling boomphf v0.5.4 [INFO] [stderr] Compiling debruijn v0.3.0 (https://github.com/10XGenomics/rust-debruijn.git#2e16852f) [INFO] [stderr] Compiling rust-htslib v0.30.0 [INFO] [stderr] Compiling 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 struct `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] ::: /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.30.0/src/bam/mod.rs:95:8 [INFO] [stderr] | [INFO] [stderr] 95 | fn header(&self) -> &HeaderView; [INFO] [stderr] | ------ [INFO] [stderr] | | [INFO] [stderr] | the method is available for `std::boxed::Box` here [INFO] [stderr] | the method is available for `std::sync::Arc` here [INFO] [stderr] | the method is available for `std::rc::Rc` here [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 arguments but 2 arguments 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] | ^^^^^^^^^^^^^^^^^^^^^^ -------- ------- supplied 2 arguments [INFO] [stderr] | | [INFO] [stderr] | expected 3 arguments [INFO] [stderr] [INFO] [stderr] error[E0599]: no method named `read` found for struct `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] ::: /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.30.0/src/bam/mod.rs:80:8 [INFO] [stderr] | [INFO] [stderr] 80 | fn read(&mut self, record: &mut record::Record) -> Result; [INFO] [stderr] | ---- [INFO] [stderr] | | [INFO] [stderr] | the method is available for `std::boxed::Box` here [INFO] [stderr] | the method is available for `std::sync::Arc` here [INFO] [stderr] | the method is available for `std::rc::Rc` here [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 struct `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] ::: /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.30.0/src/bam/mod.rs:95:8 [INFO] [stderr] | [INFO] [stderr] 95 | fn header(&self) -> &HeaderView; [INFO] [stderr] | ------ [INFO] [stderr] | | [INFO] [stderr] | the method is available for `std::boxed::Box` here [INFO] [stderr] | the method is available for `std::sync::Arc` here [INFO] [stderr] | the method is available for `std::rc::Rc` here [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 function or associated item named `from_str` found for struct `rust_htslib::bam::record::CigarString` in the current scope [INFO] [stderr] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:432:75 [INFO] [stderr] | [INFO] [stderr] 432 | bam_rec.set(&rec.name.as_bytes(), Some(&bam::record::CigarString::from_str("").unwrap()), &rec.seq.as_bytes(), &qual.as_bytes()); [INFO] [stderr] | ^^^^^^^^ function or associated item not found in `rust_htslib::bam::record::CigarString` [INFO] [stderr] [INFO] [stderr] error: aborting due to 8 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] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stderr] error: build failed [INFO] running `"docker" "inspect" "d2b838b1db42e3473c4c080f10b717781b55ab0bc395391239aaa3ee014ab05a"` [INFO] running `"docker" "rm" "-f" "d2b838b1db42e3473c4c080f10b717781b55ab0bc395391239aaa3ee014ab05a"` [INFO] [stdout] d2b838b1db42e3473c4c080f10b717781b55ab0bc395391239aaa3ee014ab05a