[INFO] cloning repository https://github.com/10XGenomics/bamtofastq [INFO] running `"git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/10XGenomics/bamtofastq" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F10XGenomics%2Fbamtofastq"` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F10XGenomics%2Fbamtofastq'... [INFO] running `"git" "rev-parse" "HEAD"` [INFO] [stdout] d3f4aa53a7236e16e59dad5c02f7887eb61ffc28 [INFO] checking 10XGenomics/bamtofastq against try#ea663bba38739867a4b75ac820991b4f5d093c3b for pr-62262-1 [INFO] running `"git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2F10XGenomics%2Fbamtofastq" "/workspace/builds/worker-9/source"` [INFO] [stderr] Cloning into '/workspace/builds/worker-9/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/10XGenomics/bamtofastq on toolchain ea663bba38739867a4b75ac820991b4f5d093c3b [INFO] running `"/workspace/cargo-home/bin/cargo" "+ea663bba38739867a4b75ac820991b4f5d093c3b" "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 /workspace/builds/worker-9/source/Cargo.toml [INFO] crate git repo https://github.com/10XGenomics/bamtofastq already has a lockfile, it will not be regenerated [INFO] running `"/workspace/cargo-home/bin/cargo" "+ea663bba38739867a4b75ac820991b4f5d093c3b" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Updating git repository `https://github.com/10XGenomics/rust-shardio.git` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded min-max-heap v1.2.0 [INFO] [stderr] Downloaded rust-htslib v0.21.0 [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/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" "+ea663bba38739867a4b75ac820991b4f5d093c3b" "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] a0757e10eb6d8a411162ad05bdad3441bdd1be7e109cf0fddf90824a2d060a6a [INFO] running `"docker" "start" "-a" "a0757e10eb6d8a411162ad05bdad3441bdd1be7e109cf0fddf90824a2d060a6a"` [INFO] [stderr] Compiling cc v1.0.20 [INFO] [stderr] Compiling serde v1.0.74 [INFO] [stderr] Compiling regex v1.0.2 [INFO] [stderr] Compiling utf8-ranges v1.0.0 [INFO] [stderr] Compiling gcc v0.3.54 [INFO] [stderr] Compiling failure_derive v0.1.2 [INFO] [stderr] Compiling termcolor v1.0.1 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Checking rustc-demangle v0.1.9 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking ieee754 v0.2.2 [INFO] [stderr] Checking min-max-heap v1.2.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking memchr v2.0.1 [INFO] [stderr] Checking rand v0.4.3 [INFO] [stderr] Compiling proc-macro2 v0.4.13 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling getopts v0.2.18 [INFO] [stderr] Compiling atty v0.2.11 [INFO] [stderr] Compiling regex-syntax v0.5.6 [INFO] [stderr] Compiling textwrap v0.10.0 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Checking crossbeam-utils v0.3.2 [INFO] [stderr] Compiling log v0.4.4 [INFO] [stderr] Compiling humantime v1.1.1 [INFO] [stderr] Compiling fs-utils v1.1.0 [INFO] [stderr] Checking itertools v0.6.5 [INFO] [stderr] Checking aho-corasick v0.6.6 [INFO] [stderr] Checking csv-core v0.1.4 [INFO] [stderr] Compiling nom v3.2.1 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling pulldown-cmark v0.0.8 [INFO] [stderr] Compiling clap v2.32.0 [INFO] [stderr] Checking uuid v0.6.5 [INFO] [stderr] Checking tempdir v0.3.7 [INFO] [stderr] Checking parking_lot_core v0.2.14 [INFO] [stderr] Checking crossbeam-epoch v0.4.3 [INFO] [stderr] Compiling quote v0.6.8 [INFO] [stderr] Checking ordered-float v0.3.0 [INFO] [stderr] Compiling lz4-sys v1.8.0 [INFO] [stderr] Checking parking_lot v0.5.5 [INFO] [stderr] Compiling skeptic v0.9.0 [INFO] [stderr] Compiling syn v0.14.9 [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] Checking crossbeam-channel v0.1.3 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Compiling lz4 v1.22.0 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Checking flate2 v1.0.2 [INFO] [stderr] Checking backtrace v0.3.9 [INFO] [stderr] Compiling env_logger v0.5.12 [INFO] [stderr] Checking os_type v2.0.0 [INFO] [stderr] Compiling synstructure v0.9.0 [INFO] [stderr] Compiling serde_derive v1.0.74 [INFO] [stderr] Checking bincode v1.0.1 [INFO] [stderr] Checking toml v0.4.6 [INFO] [stderr] Checking csv v1.0.1 [INFO] [stderr] Checking serde_bytes v0.10.4 [INFO] [stderr] Checking failure v0.1.2 [INFO] [stderr] Checking bio-types v0.2.0 [INFO] [stderr] Checking human-panic v1.0.1 [INFO] [stderr] Checking shardio v0.3.0 (https://github.com/10XGenomics/rust-shardio.git#205727d5) [INFO] [stderr] Checking docopt v1.0.0 [INFO] [stderr] Compiling rust-htslib v0.21.0 [INFO] [stderr] Checking 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>>, [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] 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 4m 00s [INFO] running `"docker" "inspect" "a0757e10eb6d8a411162ad05bdad3441bdd1be7e109cf0fddf90824a2d060a6a"` [INFO] running `"docker" "rm" "-f" "a0757e10eb6d8a411162ad05bdad3441bdd1be7e109cf0fddf90824a2d060a6a"` [INFO] [stdout] a0757e10eb6d8a411162ad05bdad3441bdd1be7e109cf0fddf90824a2d060a6a