[INFO] cloning repository https://github.com/guertinlab/seqOutBias [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/guertinlab/seqOutBias" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fguertinlab%2FseqOutBias", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fguertinlab%2FseqOutBias'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 4b0d004cf7be18e35718dc2864341316fd78077c [INFO] checking guertinlab/seqOutBias against try#05c8870159e4f328578a970e125aa76d24f03b56 for pr-76219 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fguertinlab%2FseqOutBias" "/workspace/builds/worker-2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/guertinlab/seqOutBias on toolchain 05c8870159e4f328578a970e125aa76d24f03b56 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+05c8870159e4f328578a970e125aa76d24f03b56" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/guertinlab/seqOutBias [INFO] finished tweaking git repo https://github.com/guertinlab/seqOutBias [INFO] tweaked toml for git repo https://github.com/guertinlab/seqOutBias written to /workspace/builds/worker-2/source/Cargo.toml [INFO] crate git repo https://github.com/guertinlab/seqOutBias already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+05c8870159e4f328578a970e125aa76d24f03b56" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded strsim v0.4.1 [INFO] [stderr] Downloaded assert_cmd v0.4.0 [INFO] [stderr] Downloaded rusty-cheddar v0.3.3 [INFO] [stderr] Downloaded flate2 v0.2.18 [INFO] [stderr] Downloaded rust-htslib v0.12.1 [INFO] [stderr] Downloaded escargot v0.2.0 [INFO] [stderr] Downloaded vec_map v0.4.0 [INFO] [stderr] Downloaded syntex_syntax v0.24.0 [INFO] [stderr] Downloaded clap v1.5.6 [INFO] [stderr] Downloaded predicates v0.5.2 [INFO] running `Command { std: "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" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+05c8870159e4f328578a970e125aa76d24f03b56" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] 1fe73506d2559e5f10c1601774e9af97524e01d8c7f9c6413b252ab5013dacd9 [INFO] running `Command { std: "docker" "start" "-a" "1fe73506d2559e5f10c1601774e9af97524e01d8c7f9c6413b252ab5013dacd9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "1fe73506d2559e5f10c1601774e9af97524e01d8c7f9c6413b252ab5013dacd9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1fe73506d2559e5f10c1601774e9af97524e01d8c7f9c6413b252ab5013dacd9", kill_on_drop: false }` [INFO] [stdout] 1fe73506d2559e5f10c1601774e9af97524e01d8c7f9c6413b252ab5013dacd9 [INFO] running `Command { std: "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" "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" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:d92eaeed33fa75130ca1ee6c8a01d1ffb62bac859dfdfb3450e3e5d1c0146529" "/opt/rustwide/cargo-home/bin/cargo" "+05c8870159e4f328578a970e125aa76d24f03b56" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] 375e1ee9dd259ac414b9da19264fb2303dcec18471459c9fd6ce08874ba94cbd [INFO] running `Command { std: "docker" "start" "-a" "375e1ee9dd259ac414b9da19264fb2303dcec18471459c9fd6ce08874ba94cbd", kill_on_drop: false }` [INFO] [stderr] Checking libc v0.2.43 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling winapi-build v0.1.1 [INFO] [stderr] Compiling proc-macro2 v0.4.23 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Checking winapi v0.2.8 [INFO] [stderr] Compiling version_check v0.1.5 [INFO] [stderr] Compiling gcc v0.3.45 [INFO] [stderr] Checking cfg-if v0.1.6 [INFO] [stderr] Compiling num-traits v0.2.6 [INFO] [stderr] Compiling ryu v0.2.7 [INFO] [stderr] Compiling serde v1.0.80 [INFO] [stderr] Compiling rust-htslib v0.12.1 [INFO] [stderr] Checking lazy_static v1.2.0 [INFO] [stderr] Checking percent-encoding v1.0.0 [INFO] [stderr] Checking either v1.1.0 [INFO] [stderr] Checking rustc-serialize v0.3.23 [INFO] [stderr] Compiling regex v1.0.6 [INFO] [stderr] Checking lazy_static v0.2.6 [INFO] [stderr] Checking ucd-util v0.1.3 [INFO] [stderr] Checking strsim v0.5.2 [INFO] [stderr] Checking serde v0.7.15 [INFO] [stderr] Checking num-traits v0.1.37 [INFO] [stderr] Checking itoa v0.4.3 [INFO] [stderr] Checking bitflags v0.9.1 [INFO] [stderr] Checking utf8-ranges v1.0.2 [INFO] [stderr] Checking quick-error v1.2.0 [INFO] [stderr] Compiling escargot v0.2.0 [INFO] [stderr] Checking ieee754 v0.2.2 [INFO] [stderr] Checking difference v2.0.0 [INFO] [stderr] Checking remove_dir_all v0.5.1 [INFO] [stderr] Checking fs_extra v1.1.0 [INFO] [stderr] Checking unicode-bidi v0.3.4 [INFO] [stderr] Checking thread_local v0.3.6 [INFO] [stderr] Checking itertools v0.6.0 [INFO] [stderr] Compiling kernel32-sys v0.2.2 [INFO] [stderr] Checking regex-syntax v0.6.3 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling memchr v2.1.1 [INFO] [stderr] Checking memchr v0.1.11 [INFO] [stderr] Checking rand v0.4.3 [INFO] [stderr] Checking aho-corasick v0.5.3 [INFO] [stderr] Checking idna v0.1.2 [INFO] [stderr] Checking thread-id v2.0.0 [INFO] [stderr] Checking thread_local v0.2.7 [INFO] [stderr] Checking regex v0.1.80 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling seqOutBias v1.2.0 (/opt/rustwide/workdir) [INFO] [stderr] Compiling miniz-sys v0.1.9 [INFO] [stderr] Checking aho-corasick v0.6.9 [INFO] [stderr] Compiling quote v0.6.10 [INFO] [stderr] Compiling syn v0.15.20 [INFO] [stderr] Checking url v1.7.2 [INFO] [stderr] Checking float-cmp v0.4.0 [INFO] [stderr] Checking rand v0.3.22 [INFO] [stderr] Checking tempdir v0.3.7 [INFO] [stderr] Checking tempfile v2.2.0 [INFO] [stderr] Checking flate2 v0.2.18 [INFO] [stderr] Checking docopt v0.6.86 [INFO] [stderr] Checking bincode v0.5.9 [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/tallyread.rs:75:9 [INFO] [stdout] | [INFO] [stdout] 75 | try!(result.read_sequence_data()); [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/tallyread.rs:106:40 [INFO] [stdout] | [INFO] [stdout] 106 | let (seq, pos, is_minus) = try!(parse_line(&self.line)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/tallyread.rs:141:9 [INFO] [stdout] | [INFO] [stdout] 141 | try!(self.read_sequence_data()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:47:9 [INFO] [stdout] | [INFO] [stdout] 47 | try!(writer.write_u8(super::TBL_VERSION)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:49:9 [INFO] [stdout] | [INFO] [stdout] 49 | try!(writer.write_u8(params.kmer_length)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:50:9 [INFO] [stdout] | [INFO] [stdout] 50 | try!(writer.write_u8(params.unmasked_count)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:52:9 [INFO] [stdout] | [INFO] [stdout] 52 | try!(writer.write_u8(params.plus_offset)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:53:9 [INFO] [stdout] | [INFO] [stdout] 53 | try!(writer.write_u8(params.minus_offset)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:54:9 [INFO] [stdout] | [INFO] [stdout] 54 | try!(writer.write_u16::(params.read_length)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:59:21 [INFO] [stdout] | [INFO] [stdout] 59 | try!(writer.write_u8(1)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:61:21 [INFO] [stdout] | [INFO] [stdout] 61 | try!(writer.write_u8(0)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:67:9 [INFO] [stdout] | [INFO] [stdout] 67 | try!(writer.write_u32::(blen)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:70:9 [INFO] [stdout] | [INFO] [stdout] 70 | try!(writer.write_u64::(0)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:72:9 [INFO] [stdout] | [INFO] [stdout] 72 | try!(writer.write_u64::(0)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:74:9 [INFO] [stdout] | [INFO] [stdout] 74 | try!(writer.write_u64::(0)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/write.rs:168:9 [INFO] [stdout] | [INFO] [stdout] 168 | try!(self.writer.write(&self.output[0..(total as usize)])); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:37:9 [INFO] [stdout] | [INFO] [stdout] 37 | try!(reader.seek(SeekFrom::Start(0))); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:39:23 [INFO] [stdout] | [INFO] [stdout] 39 | let version = try!(reader.read_u8()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:44:18 [INFO] [stdout] | [INFO] [stdout] 44 | let cl = try!(reader.read_u8()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:45:18 [INFO] [stdout] | [INFO] [stdout] 45 | let uc = try!(reader.read_u8()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:46:18 [INFO] [stdout] | [INFO] [stdout] 46 | let po = try!(reader.read_u8()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:47:18 [INFO] [stdout] | [INFO] [stdout] 47 | let mo = try!(reader.read_u8()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:48:18 [INFO] [stdout] | [INFO] [stdout] 48 | let rl = try!(reader.read_u16::()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:53:28 [INFO] [stdout] | [INFO] [stdout] 53 | let flag = try!(reader.read_u8()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:71:20 [INFO] [stdout] | [INFO] [stdout] 71 | let blen = try!(reader.read_u32::()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:73:22 [INFO] [stdout] | [INFO] [stdout] 73 | let offset = try!(reader.read_u64::()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:75:23 [INFO] [stdout] | [INFO] [stdout] 75 | let bufsize = try!(reader.read_u64::()) as usize; [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:77:29 [INFO] [stdout] | [INFO] [stdout] 77 | let counts_offset = try!(reader.read_u64::()); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:82:9 [INFO] [stdout] | [INFO] [stdout] 82 | try!(reader.seek(SeekFrom::Start(offset))); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:102:25 [INFO] [stdout] | [INFO] [stdout] 102 | try!(self.reader.seek(SeekFrom::Start(block.offset))); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:127:21 [INFO] [stdout] | [INFO] [stdout] 127 | try!(self.reader.seek(SeekFrom::Start(block.offset))); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:161:9 [INFO] [stdout] | [INFO] [stdout] 161 | try!(self.reader.seek(SeekFrom::Start(self.counts_offset))); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:198:9 [INFO] [stdout] | [INFO] [stdout] 198 | try!(self.reader.seek(SeekFrom::Start(block_info.offset))); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:199:9 [INFO] [stdout] | [INFO] [stdout] 199 | try!(self.reader.read(buf)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/seqtable/read.rs:226:31 [INFO] [stdout] | [INFO] [stdout] 226 | let aux = try!(self.read_block(block_info)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/counts.rs:100:16 [INFO] [stdout] | [INFO] [stdout] 100 | let file = try!(File::open(filename)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/counts.rs:111:18 [INFO] [stdout] | [INFO] [stdout] 111 | let line = try!(res); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/bigwig.rs:22:17 [INFO] [stdout] | [INFO] [stdout] 22 | let mut f = try!(File::create(filename)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/bigwig.rs:25:9 [INFO] [stdout] | [INFO] [stdout] 25 | try!(write!(f, "{}\t{}\n", chroms[index], chrom_sizes[index])); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/bigwig.rs:33:17 [INFO] [stdout] | [INFO] [stdout] 33 | let mut f = try!(File::create(filename)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/bigwig.rs:39:9 [INFO] [stdout] | [INFO] [stdout] 39 | try!(write!(f, "variableStep chrom={}\n", chrom)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/bigwig.rs:45:53 [INFO] [stdout] | [INFO] [stdout] 45 | Strand::Plus => if value.0 > 0f64 { try!(write!(f, "{}\t{}\n", pos, value.0)) }, [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/bigwig.rs:46:54 [INFO] [stdout] | [INFO] [stdout] 46 | Strand::Minus => if value.1 > 0f64 { try!(write!(f, "{}\t{}\n", pos, -value.1)) }, [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/bigwig.rs:47:33 [INFO] [stdout] | [INFO] [stdout] 47 | Strand::Both => try!(write!(f, "{}\t{}\n", pos, value.0 + value.1)), [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/bigwig.rs:78:9 [INFO] [stdout] | [INFO] [stdout] 78 | try!(write_chrom_info(chrominfo_name, chroms, chrom_sizes)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/bigwig.rs:83:9 [INFO] [stdout] | [INFO] [stdout] 83 | try!(write_wiggle(wiggle_name, chroms, counts, strand)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/scale.rs:105:21 [INFO] [stdout] | [INFO] [stdout] 105 | let mut f = try!(File::create(filename)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/scale.rs:115:25 [INFO] [stdout] | [INFO] [stdout] 115 | try!(write!(f, "{}\t{}\t{}\t.\t{}\t+\n", chrom, pos, pos + 1, value.0)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/scale.rs:118:25 [INFO] [stdout] | [INFO] [stdout] 118 | try!(write!(f, "{}\t{}\t{}\t.\t{}\t-\n", chrom, pos, pos + 1, -value.1)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/scale.rs:121:21 [INFO] [stdout] | [INFO] [stdout] 121 | try!(write!(f, "{}\t{}\t{}\t.\t{}\n", chrom, pos, pos + 1, value.0 + value.1)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/scale.rs:151:21 [INFO] [stdout] | [INFO] [stdout] 151 | try!(write_bigwig(&output_minus, &self.chroms, &self.chrom_sizes, &self.counts, Strand::Minus)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/scale.rs:157:13 [INFO] [stdout] | [INFO] [stdout] 157 | try!(write_bigwig(OsStr::new(filename), &self.chroms, &self.chrom_sizes, &self.counts, Strand::Both)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:42:1 [INFO] [stdout] | [INFO] [stdout] 42 | / pub extern fn seqoutbias_params_with_mask(kmer_mask: *const libc::c_char, plus_offset: u8, minus_offset: u8, read_length: u16) -> *mut Se... [INFO] [stdout] 43 | | let kmer_mask = unsafe { [INFO] [stdout] 44 | | assert!(!kmer_mask.is_null()); [INFO] [stdout] 45 | | CStr::from_ptr(kmer_mask).to_string_lossy().into_owned() [INFO] [stdout] ... | [INFO] [stdout] 62 | | Box::into_raw(Box::new(SeqTblParams(params))) [INFO] [stdout] 63 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = note: `#[deny(missing_abi)]` on by default [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:68:1 [INFO] [stdout] | [INFO] [stdout] 68 | / pub extern fn seqoutbias_params(kmer_size: u8, plus_offset: u8, minus_offset: u8, read_length: u16) -> *mut SeqTblParams { [INFO] [stdout] 69 | | let params = seqtable::SeqTableParams::new( [INFO] [stdout] 70 | | kmer_size, [INFO] [stdout] 71 | | plus_offset, [INFO] [stdout] ... | [INFO] [stdout] 76 | | Box::into_raw(Box::new(SeqTblParams(params))) [INFO] [stdout] 77 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:81:1 [INFO] [stdout] | [INFO] [stdout] 81 | / pub extern fn seqoutbias_free_params(ptr: *mut SeqTblParams) { [INFO] [stdout] 82 | | if ptr.is_null() { return } [INFO] [stdout] 83 | | unsafe { Box::from_raw(ptr); } [INFO] [stdout] 84 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:129:1 [INFO] [stdout] | [INFO] [stdout] 129 | / pub extern fn seqoutbias_default_config() -> Config { [INFO] [stdout] 130 | | // setup default values for config options [INFO] [stdout] 131 | | Config { [INFO] [stdout] 132 | | min_qual: 0, [INFO] [stdout] ... | [INFO] [stdout] 141 | | } [INFO] [stdout] 142 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:150:1 [INFO] [stdout] | [INFO] [stdout] 150 | / pub extern fn seqoutbias_generate_seqtbl(fasta_filename: *const libc::c_char, params: *mut SeqTblParams, output_filename: *const libc::c_... [INFO] [stdout] 151 | | let fasta_filename = unsafe { [INFO] [stdout] 152 | | assert!(!fasta_filename.is_null()); [INFO] [stdout] 153 | | CStr::from_ptr(fasta_filename).to_string_lossy().into_owned() [INFO] [stdout] ... | [INFO] [stdout] 179 | | return 0; [INFO] [stdout] 180 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:185:1 [INFO] [stdout] | [INFO] [stdout] 185 | / pub extern fn seqoutbias_create_pileup(seqtable_filename: *const libc::c_char, bam_filenames: *const *const libc::c_char, n_bams: size_t,... [INFO] [stdout] 186 | | let seqtable_filename = unsafe { [INFO] [stdout] 187 | | assert!(!seqtable_filename.is_null()); [INFO] [stdout] 188 | | CStr::from_ptr(seqtable_filename).to_string_lossy().into_owned() [INFO] [stdout] ... | [INFO] [stdout] 232 | | Box::into_raw(Box::new(PileUpData(pileup))) [INFO] [stdout] 233 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:237:1 [INFO] [stdout] | [INFO] [stdout] 237 | / pub extern fn seqoutbias_free_pileup(ptr: *mut PileUpData) { [INFO] [stdout] 238 | | if ptr.is_null() { return } [INFO] [stdout] 239 | | unsafe { Box::from_raw(ptr); } [INFO] [stdout] 240 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:246:1 [INFO] [stdout] | [INFO] [stdout] 246 | / pub extern fn seqoutbias_chrom_pileup(ptr: *mut PileUpData, chrom: *const libc::c_char, out_len: *mut size_t) -> *mut PileUpPoint { [INFO] [stdout] 247 | | let pileup = unsafe { [INFO] [stdout] 248 | | assert!(!ptr.is_null()); [INFO] [stdout] 249 | | &mut *ptr [INFO] [stdout] ... | [INFO] [stdout] 286 | | result [INFO] [stdout] 287 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:292:1 [INFO] [stdout] | [INFO] [stdout] 292 | / pub extern fn seqoutbias_query_pileup_chrom_index(ptr: *mut PileUpData, chrom: *const libc::c_char, out_index: *mut size_t) -> i32 { [INFO] [stdout] 293 | | let pileup = unsafe { [INFO] [stdout] 294 | | assert!(!ptr.is_null()); [INFO] [stdout] 295 | | &mut *ptr [INFO] [stdout] ... | [INFO] [stdout] 312 | | } [INFO] [stdout] 313 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: extern declarations without an explicit ABI are deprecated [INFO] [stdout] --> src/c_api.rs:320:1 [INFO] [stdout] | [INFO] [stdout] 320 | / pub extern fn seqoutbias_query_pileup(ptr: *mut PileUpData, chrom_index: size_t, pos: u32, out: *mut PileUpPoint) -> i32 { [INFO] [stdout] 321 | | let pileup = unsafe { [INFO] [stdout] 322 | | assert!(!ptr.is_null()); [INFO] [stdout] 323 | | &mut *ptr [INFO] [stdout] ... | [INFO] [stdout] 338 | | } [INFO] [stdout] 339 | | } [INFO] [stdout] | |_^ ABI should be specified here [INFO] [stdout] | [INFO] [stdout] = help: the default ABI is C [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `std::error::Error::description`: use the Display impl or to_string() [INFO] [stdout] --> src/seqtable/mod.rs:66:86 [INFO] [stdout] | [INFO] [stdout] 66 | println!("Error: Failed to open sequence table file '{}': {}", filename, err.description()); [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `std::error::Error::description`: use the Display impl or to_string() [INFO] [stdout] --> src/seqtable/dump.rs:52:90 [INFO] [stdout] | [INFO] [stdout] 52 | println!("Error: failed to open sequence table file '{}': {}", filename, err.description()); [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `std::error::Error::description`: use the Display impl or to_string() [INFO] [stdout] --> src/seqtable/dump.rs:94:90 [INFO] [stdout] | [INFO] [stdout] 94 | println!("Error: failed to open sequence table file '{}': {}", filename, err.description()); [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `std::error::Error::description`: use the Display impl or to_string() [INFO] [stdout] --> src/counts.rs:251:75 [INFO] [stdout] | [INFO] [stdout] 251 | println!("Error: Failed to read BED file {}: {}", filename, e.description()); [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `std::error::Error::description`: use the Display impl or to_string() [INFO] [stdout] --> src/counts.rs:292:78 [INFO] [stdout] | [INFO] [stdout] 292 | println!("Error: Failed to open BAM '{}': {}", &bamfilename, err.description()); [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `std::error::Error::description`: use the Display impl or to_string() [INFO] [stdout] --> src/counts.rs:350:89 [INFO] [stdout] | [INFO] [stdout] 350 | println!("Error: Failed to open sequence table file '{}': {}", seqfile, err.description()); [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `std::error::Error::description`: use the Display impl or to_string() [INFO] [stdout] --> src/scale.rs:207:89 [INFO] [stdout] | [INFO] [stdout] 207 | println!("Error: Failed to open sequence table file '{}': {}", seqfile, err.description()); [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated associated function `std::error::Error::description`: use the Display impl or to_string() [INFO] [stdout] --> src/scale.rs:236:82 [INFO] [stdout] | [INFO] [stdout] 236 | println!("Error: Failed to open BAM file '{}': {}", bamfile, err.description()); [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 10 previous errors; 60 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `seqOutBias`. [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stderr] error: build failed [INFO] running `Command { std: "docker" "inspect" "375e1ee9dd259ac414b9da19264fb2303dcec18471459c9fd6ce08874ba94cbd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "375e1ee9dd259ac414b9da19264fb2303dcec18471459c9fd6ce08874ba94cbd", kill_on_drop: false }` [INFO] [stdout] 375e1ee9dd259ac414b9da19264fb2303dcec18471459c9fd6ce08874ba94cbd