[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] checking wheaton5/distinguishing_kmers against master#af3c6e733a40e671550e0f0f5aeecaa13772ba56 for pr-74989
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Fdistinguishing_kmers" "/workspace/builds/worker-1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/wheaton5/distinguishing_kmers on toolchain af3c6e733a40e671550e0f0f5aeecaa13772ba56
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+af3c6e733a40e671550e0f0f5aeecaa13772ba56" "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-1/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" "+af3c6e733a40e671550e0f0f5aeecaa13772ba56" "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-1/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[INFO] the lockfile is outdated, regenerating it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" "+af3c6e733a40e671550e0f0f5aeecaa13772ba56" "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" "+af3c6e733a40e671550e0f0f5aeecaa13772ba56" "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-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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" "+af3c6e733a40e671550e0f0f5aeecaa13772ba56" "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] fa813e851c947478601226fa1cd30db606fc9b46071eb6beed41eec7f5800b42
[INFO] running `Command { std: "docker" "start" "-a" "fa813e851c947478601226fa1cd30db606fc9b46071eb6beed41eec7f5800b42", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "fa813e851c947478601226fa1cd30db606fc9b46071eb6beed41eec7f5800b42", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "fa813e851c947478601226fa1cd30db606fc9b46071eb6beed41eec7f5800b42", kill_on_drop: false }`
[INFO] [stdout] fa813e851c947478601226fa1cd30db606fc9b46071eb6beed41eec7f5800b42
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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" "RUSTFLAGS=--cap-lints=forbid" "-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" "+af3c6e733a40e671550e0f0f5aeecaa13772ba56" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] a912510171f1b1e3c40b2c8d73a7d3b7a8ccd477218729617ad675bf981eac24
[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" "a912510171f1b1e3c40b2c8d73a7d3b7a8ccd477218729617ad675bf981eac24", kill_on_drop: false }`
[INFO] [stderr]    Compiling autocfg v1.0.1
[INFO] [stderr]    Compiling libc v0.2.77
[INFO] [stderr]    Compiling proc-macro2 v1.0.21
[INFO] [stderr]    Compiling unicode-xid v0.2.1
[INFO] [stderr]    Compiling maybe-uninit v2.0.0
[INFO] [stderr]    Compiling serde_derive v1.0.116
[INFO] [stderr]    Compiling serde v1.0.116
[INFO] [stderr]     Checking scopeguard v1.1.0
[INFO] [stderr]    Compiling rayon-core v1.8.0
[INFO] [stderr]     Checking tinyvec v0.3.4
[INFO] [stderr]    Compiling glob v0.3.0
[INFO] [stderr]    Compiling ryu v1.0.5
[INFO] [stderr]    Compiling log v0.4.11
[INFO] [stderr]     Checking either v1.6.0
[INFO] [stderr]    Compiling serde_json v1.0.57
[INFO] [stderr]     Checking adler v0.2.3
[INFO] [stderr]     Checking rand_core v0.5.1
[INFO] [stderr]     Checking quick-error v1.2.3
[INFO] [stderr]     Checking percent-encoding v2.1.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking smallvec v1.4.2
[INFO] [stderr]     Checking yaml-rust v0.3.5
[INFO] [stderr]     Checking thread_local v1.0.1
[INFO] [stderr]    Compiling fs-utils v1.1.4
[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 wyhash v0.4.1
[INFO] [stderr]     Checking crc32fast v1.2.0
[INFO] [stderr]     Checking unicode-normalization v0.1.13
[INFO] [stderr]     Checking regex v1.3.9
[INFO] [stderr]    Compiling crossbeam-utils v0.7.2
[INFO] [stderr]    Compiling num-traits v0.2.12
[INFO] [stderr]    Compiling memoffset v0.5.5
[INFO] [stderr]    Compiling crossbeam-epoch v0.8.2
[INFO] [stderr]    Compiling num-integer v0.1.43
[INFO] [stderr]    Compiling num-bigint v0.3.0
[INFO] [stderr]    Compiling num-rational v0.3.0
[INFO] [stderr]    Compiling miniz_oxide v0.4.2
[INFO] [stderr]    Compiling num-iter v0.1.41
[INFO] [stderr]    Compiling rayon v1.4.0
[INFO] [stderr]    Compiling quote v1.0.7
[INFO] [stderr]     Checking num_cpus v1.13.0
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]    Compiling jobserver v0.1.21
[INFO] [stderr]     Checking clap v2.27.1
[INFO] [stderr]     Checking idna v0.2.0
[INFO] [stderr]    Compiling syn v1.0.41
[INFO] [stderr]     Checking crossbeam-channel v0.4.4
[INFO] [stderr]    Compiling cc v1.0.59
[INFO] [stderr]     Checking flate2 v1.0.17
[INFO] [stderr]     Checking crossbeam-deque v0.7.3
[INFO] [stderr]     Checking url v2.1.1
[INFO] [stderr]     Checking num-complex v0.3.0
[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 v0.3.0
[INFO] [stderr]    Compiling thiserror-impl v1.0.20
[INFO] [stderr]    Compiling derive-new v0.5.8
[INFO] [stderr]     Checking thiserror v1.0.20
[INFO] [stderr]     Checking bio-types v0.7.0
[INFO] [stderr]     Checking boomphf v0.5.5
[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<bam::Header> { 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 `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 `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" "a912510171f1b1e3c40b2c8d73a7d3b7a8ccd477218729617ad675bf981eac24", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a912510171f1b1e3c40b2c8d73a7d3b7a8ccd477218729617ad675bf981eac24", kill_on_drop: false }`
[INFO] [stdout] a912510171f1b1e3c40b2c8d73a7d3b7a8ccd477218729617ad675bf981eac24
