[INFO] updating cached repository 10XGenomics/bamtofastq [INFO] running `"git" "fetch" "--all"` [INFO] [stdout] Fetching origin [INFO] [stderr] From git://github.com/10XGenomics/bamtofastq [INFO] [stderr] * branch HEAD -> FETCH_HEAD [INFO] running `"git" "clone" "work/cache/sources/gh/10XGenomics/bamtofastq" "work/ex/beta-1.38-1/sources/1.37.0/gh/10XGenomics/bamtofastq"` [INFO] [stderr] Cloning into 'work/ex/beta-1.38-1/sources/1.37.0/gh/10XGenomics/bamtofastq'... [INFO] [stderr] done. [INFO] running `"git" "clone" "work/cache/sources/gh/10XGenomics/bamtofastq" "work/ex/beta-1.38-1/sources/beta-2019-08-13/gh/10XGenomics/bamtofastq"` [INFO] [stderr] Cloning into 'work/ex/beta-1.38-1/sources/beta-2019-08-13/gh/10XGenomics/bamtofastq'... [INFO] [stderr] done. [INFO] running `"git" "rev-parse" "HEAD"` [INFO] [stdout] d3f4aa53a7236e16e59dad5c02f7887eb61ffc28 [INFO] sha for GitHub repo 10XGenomics/bamtofastq: d3f4aa53a7236e16e59dad5c02f7887eb61ffc28 [INFO] validating manifest of 10XGenomics/bamtofastq on toolchain 1.37.0 [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+1.37.0" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] validating manifest of 10XGenomics/bamtofastq on toolchain beta-2019-08-13 [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-08-13" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] started frobbing 10XGenomics/bamtofastq [INFO] finished frobbing 10XGenomics/bamtofastq [INFO] frobbed toml for 10XGenomics/bamtofastq written to work/ex/beta-1.38-1/sources/1.37.0/gh/10XGenomics/bamtofastq/Cargo.toml [INFO] started frobbing 10XGenomics/bamtofastq [INFO] finished frobbing 10XGenomics/bamtofastq [INFO] frobbed toml for 10XGenomics/bamtofastq written to work/ex/beta-1.38-1/sources/beta-2019-08-13/gh/10XGenomics/bamtofastq/Cargo.toml [INFO] crate 10XGenomics/bamtofastq already has a lockfile, it will not be regenerated [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+1.37.0" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-08-13" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] testing 10XGenomics/bamtofastq against beta-2019-08-13 for beta-1.38-1 [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.38-1/worker-2/beta-2019-08-13:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/beta-1.38-1/sources/beta-2019-08-13/gh/10XGenomics/bamtofastq:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+beta-2019-08-13" "build" "--frozen"` [INFO] [stdout] 7f5da5f5f756818c80d7635ced0951f17dd243b6f26a1e56d203174a942a87ab [INFO] running `"docker" "start" "-a" "7f5da5f5f756818c80d7635ced0951f17dd243b6f26a1e56d203174a942a87ab"` [INFO] [stderr] Compiling cc v1.0.20 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling serde v1.0.74 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling min-max-heap v1.2.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling fs-utils v1.1.0 [INFO] [stderr] Compiling lz4-sys v1.8.0 [INFO] [stderr] Compiling itertools v0.6.5 [INFO] [stderr] Compiling pretty_assertions v0.5.1 [INFO] [stderr] Compiling csv-core v0.1.4 [INFO] [stderr] Compiling pulldown-cmark v0.0.8 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling tempfile v3.0.3 [INFO] [stderr] Compiling parking_lot_core v0.2.14 [INFO] [stderr] Compiling syn v0.14.9 [INFO] [stderr] Compiling ordered-float v0.3.0 [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 skeptic v0.9.0 [INFO] [stderr] Compiling crossbeam-channel v0.1.3 [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 libz-sys v1.0.20 [INFO] [stderr] Compiling env_logger v0.5.12 [INFO] [stderr] Compiling os_type v2.0.0 [INFO] [stderr] Compiling lz4 v1.22.0 [INFO] [stderr] Compiling synstructure v0.9.0 [INFO] [stderr] Compiling backtrace v0.3.9 [INFO] [stderr] Compiling flate2 v1.0.2 [INFO] [stderr] Compiling failure_derive v0.1.2 [INFO] [stderr] Compiling serde_derive v1.0.74 [INFO] [stderr] Compiling bincode v1.0.1 [INFO] [stderr] Compiling toml v0.4.6 [INFO] [stderr] Compiling csv v1.0.1 [INFO] [stderr] Compiling serde_bytes v0.10.4 [INFO] [stderr] Compiling failure v0.1.2 [INFO] [stderr] Compiling bio-types v0.2.0 [INFO] [stderr] Compiling shardio v0.3.0 (https://github.com/10XGenomics/rust-shardio.git#205727d5) [INFO] [stderr] Compiling docopt v1.0.0 [INFO] [stderr] Compiling human-panic v1.0.1 [INFO] [stderr] Compiling rust-htslib v0.21.0 [INFO] [stderr] Compiling bamtofastq v1.2.1 (/opt/crater/workdir) [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 3m 35s [INFO] running `"docker" "inspect" "7f5da5f5f756818c80d7635ced0951f17dd243b6f26a1e56d203174a942a87ab"` [INFO] running `"docker" "rm" "-f" "7f5da5f5f756818c80d7635ced0951f17dd243b6f26a1e56d203174a942a87ab"` [INFO] [stdout] 7f5da5f5f756818c80d7635ced0951f17dd243b6f26a1e56d203174a942a87ab [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.38-1/worker-2/beta-2019-08-13:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/beta-1.38-1/sources/beta-2019-08-13/gh/10XGenomics/bamtofastq:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+beta-2019-08-13" "test" "--frozen" "--no-run"` [INFO] [stdout] cef62ab5c6677c22539e5dbe8e8768700d34a964f3c1f3bb1f7ea865c68d5799 [INFO] running `"docker" "start" "-a" "cef62ab5c6677c22539e5dbe8e8768700d34a964f3c1f3bb1f7ea865c68d5799"` [INFO] [stderr] Compiling bamtofastq v1.2.1 (/opt/crater/workdir) [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>>, [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>>, [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>>>, [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: P) -> Box { [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>(r1: P, r2: P, si: Option

) -> Box> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn Iterator` [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, r2: Box, si: Option>) -> 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, r2: Box, si: Option>) -> 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, r2: Box, si: Option>) -> 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>>, [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>>>, [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>(ra: P, si: Option

) -> Box> { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn Iterator` [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, si: Option>) -> 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, si: Option>) -> InterleavedFastqPairIter { [INFO] [stderr] | ^^^^ help: use `dyn`: `dyn Read` [INFO] [stderr] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 13.21s [INFO] running `"docker" "inspect" "cef62ab5c6677c22539e5dbe8e8768700d34a964f3c1f3bb1f7ea865c68d5799"` [INFO] running `"docker" "rm" "-f" "cef62ab5c6677c22539e5dbe8e8768700d34a964f3c1f3bb1f7ea865c68d5799"` [INFO] [stdout] cef62ab5c6677c22539e5dbe8e8768700d34a964f3c1f3bb1f7ea865c68d5799 [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.38-1/worker-2/beta-2019-08-13:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/beta-1.38-1/sources/beta-2019-08-13/gh/10XGenomics/bamtofastq:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+beta-2019-08-13" "test" "--frozen"` [INFO] [stdout] 98013e1eee0adf2f78235a1e880f4b6caeb1cf94126edf3b0f0965e7db0c22fd [INFO] running `"docker" "start" "-a" "98013e1eee0adf2f78235a1e880f4b6caeb1cf94126edf3b0f0965e7db0c22fd"` [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 0.14s [INFO] [stderr] Running /opt/crater/target/debug/deps/bamtofastq-aee4aef93d1a440b [INFO] [stdout] [INFO] [stdout] running 4 tests [INFO] [stdout] test tests::test_cr12 ... ok [INFO] [stdout] test tests::test_lr21 ... 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" "98013e1eee0adf2f78235a1e880f4b6caeb1cf94126edf3b0f0965e7db0c22fd"` [INFO] running `"docker" "rm" "-f" "98013e1eee0adf2f78235a1e880f4b6caeb1cf94126edf3b0f0965e7db0c22fd"` [INFO] [stdout] 98013e1eee0adf2f78235a1e880f4b6caeb1cf94126edf3b0f0965e7db0c22fd