[INFO] updating cached repository https://github.com/10XGenomics/bamtofastq
[INFO] running `"git" "-c" "credential.helper=" "-c" "credential.helper=/big/crater/work/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] d3f4aa53a7236e16e59dad5c02f7887eb61ffc28
[INFO] testing 10XGenomics/bamtofastq against beta-2019-09-28 for beta-1.39-1
[INFO] running `"git" "clone" "work/cache/git-repos/https%3A%2F%2Fgithub.com%2F10XGenomics%2Fbamtofastq" "work/builds/worker-0/source"`
[INFO] [stderr] Cloning into 'work/builds/worker-0/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/10XGenomics/bamtofastq on toolchain beta-2019-09-28
[INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+beta-2019-09-28" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] started tweaking git repo https://github.com/10XGenomics/bamtofastq
[INFO] finished tweaking git repo https://github.com/10XGenomics/bamtofastq
[INFO] tweaked toml for git repo https://github.com/10XGenomics/bamtofastq written to work/builds/worker-0/source/Cargo.toml
[INFO] crate git repo https://github.com/10XGenomics/bamtofastq already has a lockfile, it will not be regenerated
[INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+beta-2019-09-28" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-0/source:/opt/rustwide/workdir:ro,Z" "-v" "/big/crater/work/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/big/crater/work/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=1000" "-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-2019-09-28" "build" "--frozen"`
[INFO] [stdout] d493f061ec8a44ecb13b1f47b213b6c06560e621613fb8d0f4c8cafe41e5a923
[INFO] running `"docker" "start" "-a" "d493f061ec8a44ecb13b1f47b213b6c06560e621613fb8d0f4c8cafe41e5a923"`
[INFO] [stderr]    Compiling serde v1.0.74
[INFO] [stderr]    Compiling termcolor v1.0.1
[INFO] [stderr]    Compiling bindgen v0.36.1
[INFO] [stderr]    Compiling min-max-heap v1.2.0
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling ieee754 v0.2.2
[INFO] [stderr]    Compiling linear-map v1.2.0
[INFO] [stderr]    Compiling memchr v2.0.1
[INFO] [stderr]    Compiling memchr v1.0.2
[INFO] [stderr]    Compiling which v1.0.5
[INFO] [stderr]    Compiling clang-sys v0.22.0
[INFO] [stderr]    Compiling libloading v0.5.0
[INFO] [stderr]    Compiling backtrace-sys v0.1.24
[INFO] [stderr]    Compiling miniz-sys v0.1.10
[INFO] [stderr]    Compiling lz4-sys v1.8.0
[INFO] [stderr]    Compiling libz-sys v1.0.20
[INFO] [stderr]    Compiling fs-utils v1.1.0
[INFO] [stderr]    Compiling pretty_assertions v0.5.1
[INFO] [stderr]    Compiling itertools v0.6.5
[INFO] [stderr]    Compiling pulldown-cmark v0.0.8
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling nom v3.2.1
[INFO] [stderr]    Compiling aho-corasick v0.6.6
[INFO] [stderr]    Compiling csv-core v0.1.4
[INFO] [stderr]    Compiling parking_lot_core v0.2.14
[INFO] [stderr]    Compiling ordered-float v0.3.0
[INFO] [stderr]    Compiling serde_derive v1.0.74
[INFO] [stderr]    Compiling synstructure v0.9.0
[INFO] [stderr]    Compiling regex v1.0.2
[INFO] [stderr]    Compiling regex v0.2.11
[INFO] [stderr]    Compiling parking_lot v0.5.5
[INFO] [stderr]    Compiling flate2 v1.0.2
[INFO] [stderr]    Compiling skeptic v0.9.0
[INFO] [stderr]    Compiling backtrace v0.3.9
[INFO] [stderr]    Compiling crossbeam-channel v0.1.3
[INFO] [stderr]    Compiling cexpr v0.2.3
[INFO] [stderr]    Compiling failure_derive v0.1.2
[INFO] [stderr]    Compiling lz4 v1.22.0
[INFO] [stderr]    Compiling os_type v2.0.0
[INFO] [stderr]    Compiling env_logger v0.5.12
[INFO] [stderr]    Compiling failure v0.1.2
[INFO] [stderr]    Compiling bincode v1.0.1
[INFO] [stderr]    Compiling toml v0.4.6
[INFO] [stderr]    Compiling bio-types v0.2.0
[INFO] [stderr]    Compiling csv v1.0.1
[INFO] [stderr]    Compiling docopt v1.0.0
[INFO] [stderr]    Compiling serde_bytes v0.10.4
[INFO] [stderr]    Compiling shardio v0.3.0 (https://github.com/10XGenomics/rust-shardio.git#205727d5)
[INFO] [stderr]    Compiling human-panic v1.0.1
[INFO] [stderr]    Compiling rust-htslib v0.21.0
[INFO] [stderr]    Compiling bamtofastq v1.2.1 (/opt/rustwide/workdir)
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/main.rs:950:23
[INFO] [stderr]     |
[INFO] [stderr] 950 |             let bxi = try!(bx_index::BxIndex::new(args.arg_bam));
[INFO] [stderr]     |                       ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(deprecated)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/main.rs:951:27
[INFO] [stderr]     |
[INFO] [stderr] 951 |             let bx_iter = try!(BxListIter::from_path(args.flag_bx_list.unwrap(), bxi, bam));
[INFO] [stderr]     |                           ^^^
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/main.rs:964:20
[INFO] [stderr]     |
[INFO] [stderr] 964 |     let tmp_file = try!(NamedTempFile::new_in(&fq.out_path));
[INFO] [stderr]     |                    ^^^
[INFO] [stderr] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 2m 00s
[INFO] running `"docker" "inspect" "d493f061ec8a44ecb13b1f47b213b6c06560e621613fb8d0f4c8cafe41e5a923"`
[INFO] running `"docker" "rm" "-f" "d493f061ec8a44ecb13b1f47b213b6c06560e621613fb8d0f4c8cafe41e5a923"`
[INFO] [stdout] d493f061ec8a44ecb13b1f47b213b6c06560e621613fb8d0f4c8cafe41e5a923
[INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-0/source:/opt/rustwide/workdir:ro,Z" "-v" "/big/crater/work/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/big/crater/work/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=1000" "-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-2019-09-28" "test" "--frozen" "--no-run"`
[INFO] [stdout] 86af02ab405bd8739d3720f701c86e806d0f6ef88be02ab8d2fca3e55f6bbfcd
[INFO] running `"docker" "start" "-a" "86af02ab405bd8739d3720f701c86e806d0f6ef88be02ab8d2fca3e55f6bbfcd"`
[INFO] [stderr]    Compiling bamtofastq v1.2.1 (/opt/rustwide/workdir)
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/main.rs:950:23
[INFO] [stderr]     |
[INFO] [stderr] 950 |             let bxi = try!(bx_index::BxIndex::new(args.arg_bam));
[INFO] [stderr]     |                       ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(deprecated)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/main.rs:951:27
[INFO] [stderr]     |
[INFO] [stderr] 951 |             let bx_iter = try!(BxListIter::from_path(args.flag_bx_list.unwrap(), bxi, bam));
[INFO] [stderr]     |                           ^^^
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead
[INFO] [stderr]    --> src/main.rs:964:20
[INFO] [stderr]     |
[INFO] [stderr] 964 |     let tmp_file = try!(NamedTempFile::new_in(&fq.out_path));
[INFO] [stderr]     |                    ^^^
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:38:29
[INFO] [stderr]    |
[INFO] [stderr] 38 |     r1: Lines<BufReader<Box<Read>>>,
[INFO] [stderr]    |                             ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(bare_trait_objects)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:39:29
[INFO] [stderr]    |
[INFO] [stderr] 39 |     r2: Lines<BufReader<Box<Read>>>,
[INFO] [stderr]    |                             ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:40:36
[INFO] [stderr]    |
[INFO] [stderr] 40 |     si: Option<Lines<BufReader<Box<Read>>>>,
[INFO] [stderr]    |                                    ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:43:47
[INFO] [stderr]    |
[INFO] [stderr] 43 | pub fn open_w_gz<P: AsRef<Path>>(p: P) -> Box<Read> {
[INFO] [stderr]    |                                               ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:57:81
[INFO] [stderr]    |
[INFO] [stderr] 57 | pub fn open_fastq_pair_iter<P: AsRef<Path>>(r1: P, r2: P, si: Option<P>) -> Box<Iterator<Item=RawReadSet>> {
[INFO] [stderr]    |                                                                                 ^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn Iterator<Item=RawReadSet>`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:67:25
[INFO] [stderr]    |
[INFO] [stderr] 67 |     pub fn init(r1: Box<Read>, r2: Box<Read>, si: Option<Box<Read>>) -> FastqPairIter {
[INFO] [stderr]    |                         ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:67:40
[INFO] [stderr]    |
[INFO] [stderr] 67 |     pub fn init(r1: Box<Read>, r2: Box<Read>, si: Option<Box<Read>>) -> FastqPairIter {
[INFO] [stderr]    |                                        ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:67:62
[INFO] [stderr]    |
[INFO] [stderr] 67 |     pub fn init(r1: Box<Read>, r2: Box<Read>, si: Option<Box<Read>>) -> FastqPairIter {
[INFO] [stderr]    |                                                              ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:95:29
[INFO] [stderr]    |
[INFO] [stderr] 95 |     ra: Lines<BufReader<Box<Read>>>,
[INFO] [stderr]    |                             ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:96:36
[INFO] [stderr]    |
[INFO] [stderr] 96 |     si: Option<Lines<BufReader<Box<Read>>>>,
[INFO] [stderr]    |                                    ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]   --> src/fastq_reader.rs:99:86
[INFO] [stderr]    |
[INFO] [stderr] 99 | pub fn open_interleaved_fastq_pair_iter<P: AsRef<Path>>(ra: P, si: Option<P>) -> Box<Iterator<Item=RawReadSet>> {
[INFO] [stderr]    |                                                                                      ^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn Iterator<Item=RawReadSet>`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]    --> src/fastq_reader.rs:109:25
[INFO] [stderr]     |
[INFO] [stderr] 109 |     pub fn init(ra: Box<Read>, si: Option<Box<Read>>) -> InterleavedFastqPairIter {
[INFO] [stderr]     |                         ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated
[INFO] [stderr]    --> src/fastq_reader.rs:109:47
[INFO] [stderr]     |
[INFO] [stderr] 109 |     pub fn init(ra: Box<Read>, si: Option<Box<Read>>) -> InterleavedFastqPairIter {
[INFO] [stderr]     |                                               ^^^^ help: use `dyn`: `dyn Read`
[INFO] [stderr] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 6.97s
[INFO] running `"docker" "inspect" "86af02ab405bd8739d3720f701c86e806d0f6ef88be02ab8d2fca3e55f6bbfcd"`
[INFO] running `"docker" "rm" "-f" "86af02ab405bd8739d3720f701c86e806d0f6ef88be02ab8d2fca3e55f6bbfcd"`
[INFO] [stdout] 86af02ab405bd8739d3720f701c86e806d0f6ef88be02ab8d2fca3e55f6bbfcd
[INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-0/source:/opt/rustwide/workdir:ro,Z" "-v" "/big/crater/work/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/big/crater/work/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=1000" "-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-2019-09-28" "test" "--frozen"`
[INFO] [stdout] 4bd427e0263321f7d26e539003f0afab43edcca4aaf8721efa8fb91545dcef4c
[INFO] running `"docker" "start" "-a" "4bd427e0263321f7d26e539003f0afab43edcca4aaf8721efa8fb91545dcef4c"`
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 0.90s
[INFO] [stderr]      Running /opt/rustwide/target/debug/deps/bamtofastq-e4a3bed893db8909
[INFO] [stdout] 
[INFO] [stdout] running 4 tests
[INFO] [stdout] test tests::test_lr21 ... ok
[INFO] [stdout] test tests::test_cr12 ... ok
[INFO] [stdout] test tests::test_lr20 ... ok
[INFO] [stdout] test tests::test_cr12_v1 ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out
[INFO] [stdout] 
[INFO] running `"docker" "inspect" "4bd427e0263321f7d26e539003f0afab43edcca4aaf8721efa8fb91545dcef4c"`
[INFO] running `"docker" "rm" "-f" "4bd427e0263321f7d26e539003f0afab43edcca4aaf8721efa8fb91545dcef4c"`
[INFO] [stdout] 4bd427e0263321f7d26e539003f0afab43edcca4aaf8721efa8fb91545dcef4c