[INFO] cloning repository https://github.com/wheaton5/distinguishing_kmers [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/wheaton5/distinguishing_kmers" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Fdistinguishing_kmers", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Fdistinguishing_kmers'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 956d14d256c7fea54b7e8b072fc67bc99e98e594 [INFO] documenting wheaton5/distinguishing_kmers against beta-2020-08-29 for beta-1.47-rustdoc-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Fdistinguishing_kmers" "/workspace/builds/worker-10/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-10/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/wheaton5/distinguishing_kmers on toolchain beta-2020-08-29 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-08-29" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [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-10/source/Cargo.toml [INFO] crate git repo https://github.com/wheaton5/distinguishing_kmers already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-08-29" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [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-10/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 [INFO] the lockfile is outdated, regenerating it [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-08-29" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }` [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 `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-08-29" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/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" "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" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-08-29" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 598f1c7e6c8ac69365b4add65750e4639b026f9e1cd204a9cad8a223e4c3df06 [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" "598f1c7e6c8ac69365b4add65750e4639b026f9e1cd204a9cad8a223e4c3df06", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "598f1c7e6c8ac69365b4add65750e4639b026f9e1cd204a9cad8a223e4c3df06", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "598f1c7e6c8ac69365b4add65750e4639b026f9e1cd204a9cad8a223e4c3df06", kill_on_drop: false }` [INFO] [stdout] 598f1c7e6c8ac69365b4add65750e4639b026f9e1cd204a9cad8a223e4c3df06 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-10/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" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-08-29" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 86ab215f1c5ef6270c0adaa9007feae90282589a0eed1af684357be6fdd84173 [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" "86ab215f1c5ef6270c0adaa9007feae90282589a0eed1af684357be6fdd84173", kill_on_drop: false }` [INFO] [stderr] Compiling syn v1.0.39 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Checking rand_core v0.5.1 [INFO] [stderr] Checking bit-vec v0.6.2 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Compiling rayon-core v1.8.0 [INFO] [stderr] Checking itertools v0.9.0 [INFO] [stderr] Checking textwrap v0.9.0 [INFO] [stderr] Checking bloom v0.3.2 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking idna v0.2.0 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Checking num-integer v0.1.43 [INFO] [stderr] Checking num-complex v0.3.0 [INFO] [stderr] Compiling rayon v1.4.0 [INFO] [stderr] Checking flate2 v1.0.17 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking wyhash v0.4.1 [INFO] [stderr] Checking clap v2.27.1 [INFO] [stderr] Compiling cc v1.0.59 [INFO] [stderr] Checking bit-set v0.5.2 [INFO] [stderr] Checking num-bigint v0.3.0 [INFO] [stderr] Checking num-iter v0.1.41 [INFO] [stderr] Checking url v2.1.1 [INFO] [stderr] Compiling openssl-src v111.10.2+1.1.1g [INFO] [stderr] Compiling openssl-sys v0.9.58 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.16 [INFO] [stderr] Compiling curl-sys v0.4.36+curl-7.71.1 [INFO] [stderr] Compiling hts-sys v1.10.3 [INFO] [stderr] Checking num-rational v0.3.0 [INFO] [stderr] Checking num v0.3.0 [INFO] [stderr] Compiling serde_derive v1.0.115 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling thiserror-impl v1.0.20 [INFO] [stderr] Checking thiserror v1.0.20 [INFO] [stderr] Checking serde v1.0.115 [INFO] [stderr] Checking bio-types v0.7.0 [INFO] [stderr] Checking boomphf v0.5.5 [INFO] [stderr] Checking serde_json v1.0.57 [INFO] [stderr] Checking debruijn v0.3.2 (https://github.com/10XGenomics/rust-debruijn.git#39e6c0a6) [INFO] [stderr] Checking rust-htslib v0.32.0 [INFO] [stderr] Checking dna_io v0.1.0 (https://github.com/wheaton5/dna_io.git#a640f47b) [INFO] [stdout] error[E0432]: unresolved import `rust_htslib::sam` [INFO] [stdout] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:15:5 [INFO] [stdout] | [INFO] [stdout] 15 | use rust_htslib::sam; [INFO] [stdout] | ^^^^^^^^^^^^^--- [INFO] [stdout] | | | [INFO] [stdout] | | help: a similar name exists in the module: `bam` [INFO] [stdout] | no `sam` in the root [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved imports `rust_htslib::prelude`, `DnaReader`, `DnaRecord`, `DnaWriter`, `DnaWrite`, `flush` [INFO] [stdout] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:17:18 [INFO] [stdout] | [INFO] [stdout] 17 | use rust_htslib::prelude::*; [INFO] [stdout] | ^^^^^^^ could not find `prelude` in `rust_htslib` [INFO] [stdout] ... [INFO] [stdout] 442 | use DnaReader; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 443 | #[allow(unused_imports)] [INFO] [stdout] 444 | use DnaRecord; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 445 | #[allow(unused_imports)] [INFO] [stdout] 446 | use DnaWriter; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] 447 | use DnaWrite; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 450 | use flush; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: could not find `ReadError` in `bam` [INFO] [stdout] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:360:22 [INFO] [stdout] | [INFO] [stdout] 360 | Err(bam::ReadError::NoMoreRecord) => return None, [INFO] [stdout] | ^^^^^^^^^ could not find `ReadError` in `bam` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `header` found for struct `rust_htslib::bam::Reader` in the current scope [INFO] [stdout] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:350:52 [INFO] [stdout] | [INFO] [stdout] 350 | let header = bam::Header::from_template(template.header()); [INFO] [stdout] | ^^^^^^ private field, not a method [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: the following trait is implemented but not in scope; perhaps add a `use` for it: [INFO] [stdout] | [INFO] [stdout] 4 | use rust_htslib::bam::Read; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0061]: this function takes 3 arguments but 2 arguments were supplied [INFO] [stdout] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:351:17 [INFO] [stdout] | [INFO] [stdout] 351 | let mut bam = bam::Writer::from_path(filename, &header).expect("could not open bam for writing"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ -------- ------- supplied 2 arguments [INFO] [stdout] | | [INFO] [stdout] | expected 3 arguments [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `read` found for struct `rust_htslib::bam::Reader` in the current scope [INFO] [stdout] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:359:21 [INFO] [stdout] | [INFO] [stdout] 359 | match self.reader.read(&mut record) { [INFO] [stdout] | ^^^^ method not found in `rust_htslib::bam::Reader` [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: the following trait is implemented but not in scope; perhaps add a `use` for it: [INFO] [stdout] | [INFO] [stdout] 4 | use rust_htslib::bam::Read; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `header` found for struct `rust_htslib::bam::Reader` in the current scope [INFO] [stdout] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:372:91 [INFO] [stdout] | [INFO] [stdout] 372 | fn header(&self) -> Option { Some(bam::Header::from_template(self.reader.header())) } [INFO] [stdout] | ^^^^^^ private field, not a method [INFO] [stdout] | [INFO] [stdout] = help: items from traits can only be used if the trait is in scope [INFO] [stdout] help: the following trait is implemented but not in scope; perhaps add a `use` for it: [INFO] [stdout] | [INFO] [stdout] 4 | use rust_htslib::bam::Read; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no function or associated item named `from_str` found for struct `rust_htslib::bam::record::CigarString` in the current scope [INFO] [stdout] --> /opt/rustwide/cargo-home/git/checkouts/dna_io-ca28cc8dc9331b22/a640f47/src/lib.rs:432:75 [INFO] [stdout] | [INFO] [stdout] 432 | bam_rec.set(&rec.name.as_bytes(), Some(&bam::record::CigarString::from_str("").unwrap()), &rec.seq.as_bytes(), &qual.as_bytes()); [INFO] [stdout] | ^^^^^^^^ function or associated item not found in `rust_htslib::bam::record::CigarString` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 8 previous errors [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0061, E0432, E0433, E0599. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0061`. [INFO] [stdout] [INFO] [stderr] error: could not compile `dna_io`. [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [INFO] running `Command { std: "docker" "inspect" "86ab215f1c5ef6270c0adaa9007feae90282589a0eed1af684357be6fdd84173", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "86ab215f1c5ef6270c0adaa9007feae90282589a0eed1af684357be6fdd84173", kill_on_drop: false }` [INFO] [stdout] 86ab215f1c5ef6270c0adaa9007feae90282589a0eed1af684357be6fdd84173