[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] checking wheaton5/distinguishing_kmers against master#209b2be09fcaff937480d1fbbe8b31646e361c7a for pr-70917
[INFO] running `"git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Fdistinguishing_kmers" "/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/distinguishing_kmers on toolchain 209b2be09fcaff937480d1fbbe8b31646e361c7a
[INFO] running `"/workspace/cargo-home/bin/cargo" "+209b2be09fcaff937480d1fbbe8b31646e361c7a" "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-2/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" "+209b2be09fcaff937480d1fbbe8b31646e361c7a" "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] [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[INFO] the lockfile is outdated, regenerating it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" "+209b2be09fcaff937480d1fbbe8b31646e361c7a" "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" "+209b2be09fcaff937480d1fbbe8b31646e361c7a" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[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" "+209b2be09fcaff937480d1fbbe8b31646e361c7a" "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] ddc23467b5a20137c120c52a538e08260894acdd60cb608672ad7e35f1b9a455
[INFO] running `"docker" "start" "-a" "ddc23467b5a20137c120c52a538e08260894acdd60cb608672ad7e35f1b9a455"`
[INFO] [stderr]    Compiling bindgen v0.53.2
[INFO] [stderr]     Checking rand_core v0.4.2
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]    Compiling curl-sys v0.4.30+curl-7.69.1
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking bloom v0.3.2
[INFO] [stderr]     Checking bzip2-sys v0.1.8+1.0.8
[INFO] [stderr]     Checking libz-sys v1.0.25
[INFO] [stderr]    Compiling libloading v0.5.2
[INFO] [stderr]     Checking lzma-sys v0.1.15
[INFO] [stderr]     Checking flate2 v1.0.14
[INFO] [stderr]     Checking clap v2.27.1
[INFO] [stderr]     Checking wyhash v0.3.0
[INFO] [stderr]    Compiling serde_derive v1.0.106
[INFO] [stderr]    Compiling snafu-derive v0.6.6
[INFO] [stderr]    Compiling derive-new v0.5.8
[INFO] [stderr]    Compiling clang-sys v0.29.3
[INFO] [stderr]     Checking rayon-core v1.7.0
[INFO] [stderr]     Checking rayon v1.3.0
[INFO] [stderr]     Checking snafu v0.6.0
[INFO] [stderr]     Checking serde v1.0.106
[INFO] [stderr]    Compiling hts-sys v1.10.2
[INFO] [stderr]     Checking bio-types v0.6.0
[INFO] [stderr]     Checking serde_json v1.0.51
[INFO] [stderr]     Checking boomphf v0.5.4
[INFO] [stderr]     Checking debruijn v0.3.0 (https://github.com/10XGenomics/rust-debruijn.git#2e16852f)
[INFO] [stderr]     Checking rust-htslib v0.30.0
[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 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<rust_htslib::bam::Reader>` here
[INFO] [stderr]     |        the method is available for `std::sync::Arc<rust_htslib::bam::Reader>` here
[INFO] [stderr]     |        the method is available for `std::rc::Rc<rust_htslib::bam::Reader>` 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<bool>;
[INFO] [stderr]     |        ----
[INFO] [stderr]     |        |
[INFO] [stderr]     |        the method is available for `std::boxed::Box<rust_htslib::bam::Reader>` here
[INFO] [stderr]     |        the method is available for `std::sync::Arc<rust_htslib::bam::Reader>` here
[INFO] [stderr]     |        the method is available for `std::rc::Rc<rust_htslib::bam::Reader>` 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<bam::Header> { 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<rust_htslib::bam::Reader>` here
[INFO] [stderr]     |        the method is available for `std::sync::Arc<rust_htslib::bam::Reader>` here
[INFO] [stderr]     |        the method is available for `std::rc::Rc<rust_htslib::bam::Reader>` 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] running `"docker" "inspect" "ddc23467b5a20137c120c52a538e08260894acdd60cb608672ad7e35f1b9a455"`
[INFO] running `"docker" "rm" "-f" "ddc23467b5a20137c120c52a538e08260894acdd60cb608672ad7e35f1b9a455"`
[INFO] [stdout] ddc23467b5a20137c120c52a538e08260894acdd60cb608672ad7e35f1b9a455
