[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-1.37-6/sources/1.36.0/gh/10XGenomics/bamtofastq"` [INFO] [stderr] Cloning into 'work/ex/beta-1.37-6/sources/1.36.0/gh/10XGenomics/bamtofastq'... [INFO] [stderr] done. [INFO] running `"git" "clone" "work/cache/sources/gh/10XGenomics/bamtofastq" "work/ex/beta-1.37-6/sources/beta-2019-07-23/gh/10XGenomics/bamtofastq"` [INFO] [stderr] Cloning into 'work/ex/beta-1.37-6/sources/beta-2019-07-23/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 1.36.0 [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+1.36.0" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] validating manifest of 10XGenomics/bamtofastq on toolchain beta-2019-07-23 [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-07-23" "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-1.37-6/sources/1.36.0/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-1.37-6/sources/beta-2019-07-23/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" "+1.36.0" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-07-23" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] testing 10XGenomics/bamtofastq against beta-2019-07-23 for beta-1.37-6 [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.37-6/worker-7/beta-2019-07-23:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/beta-1.37-6/sources/beta-2019-07-23/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-2019-07-23" "build" "--frozen"` [INFO] [stdout] b8e0362b21e95205055bb04fc0e7f26bc1dddda082fdf18da43393e28d8caafe [INFO] running `"docker" "start" "-a" "b8e0362b21e95205055bb04fc0e7f26bc1dddda082fdf18da43393e28d8caafe"` [INFO] [stderr] Compiling cc v1.0.20 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling serde v1.0.74 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling min-max-heap v1.2.0 [INFO] [stderr] Compiling ieee754 v0.2.2 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling proc-macro2 v0.3.5 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Compiling fs-utils v1.1.0 [INFO] [stderr] Compiling lz4-sys v1.8.0 [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 nom v3.2.1 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling ordered-float v0.3.0 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling serde_derive v1.0.74 [INFO] [stderr] Compiling crossbeam-channel v0.1.3 [INFO] [stderr] Compiling quote v0.5.2 [INFO] [stderr] Compiling libloading v0.5.0 [INFO] [stderr] Compiling backtrace-sys v0.1.24 [INFO] [stderr] Compiling libz-sys v1.0.20 [INFO] [stderr] Compiling miniz-sys v0.1.10 [INFO] [stderr] Compiling skeptic v0.9.0 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Compiling lz4 v1.22.0 [INFO] [stderr] Compiling backtrace v0.3.9 [INFO] [stderr] Compiling flate2 v1.0.2 [INFO] [stderr] Compiling failure v0.1.2 [INFO] [stderr] Compiling os_type v2.0.0 [INFO] [stderr] Compiling bio-types v0.2.0 [INFO] [stderr] Compiling toml v0.4.6 [INFO] [stderr] Compiling bincode v1.0.1 [INFO] [stderr] Compiling serde_bytes v0.10.4 [INFO] [stderr] Compiling docopt v1.0.0 [INFO] [stderr] Compiling csv v1.0.1 [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/crater/workdir) [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 3m 17s [INFO] running `"docker" "inspect" "b8e0362b21e95205055bb04fc0e7f26bc1dddda082fdf18da43393e28d8caafe"` [INFO] running `"docker" "rm" "-f" "b8e0362b21e95205055bb04fc0e7f26bc1dddda082fdf18da43393e28d8caafe"` [INFO] [stdout] b8e0362b21e95205055bb04fc0e7f26bc1dddda082fdf18da43393e28d8caafe [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.37-6/worker-7/beta-2019-07-23:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/beta-1.37-6/sources/beta-2019-07-23/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-2019-07-23" "test" "--frozen" "--no-run"` [INFO] [stdout] f8dd7485d9005219a7927f51bee5bfe119738f0c495cde3537a9c71eeb8eaa63 [INFO] running `"docker" "start" "-a" "f8dd7485d9005219a7927f51bee5bfe119738f0c495cde3537a9c71eeb8eaa63"` [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" "f8dd7485d9005219a7927f51bee5bfe119738f0c495cde3537a9c71eeb8eaa63"` [INFO] running `"docker" "rm" "-f" "f8dd7485d9005219a7927f51bee5bfe119738f0c495cde3537a9c71eeb8eaa63"` [INFO] [stdout] f8dd7485d9005219a7927f51bee5bfe119738f0c495cde3537a9c71eeb8eaa63 [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.37-6/worker-7/beta-2019-07-23:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/beta-1.37-6/sources/beta-2019-07-23/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-2019-07-23" "test" "--frozen"` [INFO] [stdout] 800c6b8174e9c4a71a1543bdbd591e5889b222d0f82f694564ff881c185b471b [INFO] running `"docker" "start" "-a" "800c6b8174e9c4a71a1543bdbd591e5889b222d0f82f694564ff881c185b471b"` [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 0.08s [INFO] [stderr] Running /opt/crater/target/debug/deps/bamtofastq-1b592ccd652cf0ac [INFO] [stdout] [INFO] [stdout] running 4 tests [INFO] [stdout] test tests::test_lr20 ... ok [INFO] [stdout] test tests::test_cr12 ... ok [INFO] [stdout] test tests::test_lr21 ... 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" "800c6b8174e9c4a71a1543bdbd591e5889b222d0f82f694564ff881c185b471b"` [INFO] running `"docker" "rm" "-f" "800c6b8174e9c4a71a1543bdbd591e5889b222d0f82f694564ff881c185b471b"` [INFO] [stdout] 800c6b8174e9c4a71a1543bdbd591e5889b222d0f82f694564ff881c185b471b