[INFO] fetching crate libprosic 0.7.3... [INFO] checking libprosic-0.7.3 against master#ab869e094a907cc5d19b4080f22eccaf347f1f95 for pr-129604 [INFO] extracting crate libprosic 0.7.3 into /workspace/builds/worker-3-tc1/source [INFO] validating manifest of crates.io crate libprosic 0.7.3 on toolchain ab869e094a907cc5d19b4080f22eccaf347f1f95 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ab869e094a907cc5d19b4080f22eccaf347f1f95" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate libprosic 0.7.3 [INFO] finished tweaking crates.io crate libprosic 0.7.3 [INFO] tweaked toml for crates.io crate libprosic 0.7.3 written to /workspace/builds/worker-3-tc1/source/Cargo.toml [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ab869e094a907cc5d19b4080f22eccaf347f1f95" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Locking 168 packages to latest compatible versions [INFO] [stderr] Adding GSL v1.1.0 (latest: v7.0.0) [INFO] [stderr] Adding aho-corasick v0.5.3 (latest: v1.1.3) [INFO] [stderr] Adding aho-corasick v0.6.10 (latest: v1.1.3) [INFO] [stderr] Adding approx v0.1.1 (latest: v0.5.1) [INFO] [stderr] Adding approx v0.3.2 (latest: v0.5.1) [INFO] [stderr] Adding base64 v0.9.3 (latest: v0.22.1) [INFO] [stderr] Adding bindgen v0.36.1 (latest: v0.70.1) [INFO] [stderr] Adding bio v0.24.0 (latest: v2.0.1) [INFO] [stderr] Adding bit-set v0.5.3 (latest: v0.8.0) [INFO] [stderr] Adding bit-vec v0.6.3 (latest: v0.8.0) [INFO] [stderr] Adding bitflags v0.9.1 (latest: v2.6.0) [INFO] [stderr] Adding bitflags v1.3.2 (latest: v2.6.0) [INFO] [stderr] Adding bv v0.10.0 (latest: v0.11.1) [INFO] [stderr] Adding bytecount v0.3.2 (latest: v0.6.8) [INFO] [stderr] Adding c_vec v1.0.12 (latest: v2.0.0) [INFO] [stderr] Adding cached v0.7.0 (latest: v0.53.1) [INFO] [stderr] Adding cexpr v0.2.3 (latest: v0.6.0) [INFO] [stderr] Adding cfg-if v0.1.10 (latest: v1.0.0) [INFO] [stderr] Adding clang-sys v0.22.0 (latest: v1.8.1) [INFO] [stderr] Adding clap v2.34.0 (latest: v4.5.16) [INFO] [stderr] Adding derive-new v0.6.0 (latest: v0.7.0) [INFO] [stderr] Adding env_logger v0.3.5 (latest: v0.11.5) [INFO] [stderr] Adding env_logger v0.5.13 (latest: v0.11.5) [INFO] [stderr] Adding fern v0.4.4 (latest: v0.6.2) [INFO] [stderr] Adding flate2 v0.2.20 (latest: v1.0.33) [INFO] [stderr] Adding glob v0.2.11 (latest: v0.3.1) [INFO] [stderr] Adding hermit-abi v0.1.19 (latest: v0.4.0) [INFO] [stderr] Adding hermit-abi v0.3.9 (latest: v0.4.0) [INFO] [stderr] Adding humantime v1.3.0 (latest: v2.1.0) [INFO] [stderr] Adding hyper v0.10.16 (latest: v1.4.1) [INFO] [stderr] Adding idna v0.1.5 (latest: v1.0.2) [INFO] [stderr] Adding itertools v0.5.10 (latest: v0.13.0) [INFO] [stderr] Adding itertools v0.6.5 (latest: v0.13.0) [INFO] [stderr] Adding itertools v0.7.11 (latest: v0.13.0) [INFO] [stderr] Adding language-tags v0.2.2 (latest: v0.3.2) [INFO] [stderr] Adding lazy_static v0.2.11 (latest: v1.5.0) [INFO] [stderr] Adding libloading v0.5.2 (latest: v0.8.5) [INFO] [stderr] Adding log v0.3.9 (latest: v0.4.22) [INFO] [stderr] Adding matrixmultiply v0.1.15 (latest: v0.3.9) [INFO] [stderr] Adding memchr v0.1.11 (latest: v2.7.4) [INFO] [stderr] Adding memchr v1.0.2 (latest: v2.7.4) [INFO] [stderr] Adding mime v0.2.6 (latest: v0.3.17) [INFO] [stderr] Adding multimap v0.4.0 (latest: v0.10.0) [INFO] [stderr] Adding ndarray v0.6.10 (latest: v0.16.1) [INFO] [stderr] Adding ndarray v0.12.1 (latest: v0.16.1) [INFO] [stderr] Adding nom v3.2.1 (latest: v7.1.3) [INFO] [stderr] Adding num v0.1.42 (latest: v0.4.3) [INFO] [stderr] Adding num-complex v0.1.43 (latest: v0.4.6) [INFO] [stderr] Adding num-complex v0.2.4 (latest: v0.4.6) [INFO] [stderr] Adding num-traits v0.1.43 (latest: v0.2.19) [INFO] [stderr] Adding ordered-float v1.1.1 (latest: v4.2.2) [INFO] [stderr] Adding peeking_take_while v0.1.2 (latest: v1.0.0) [INFO] [stderr] Adding percent-encoding v1.0.1 (latest: v2.3.1) [INFO] [stderr] Adding proc-macro2 v0.3.5 (latest: v1.0.86) [INFO] [stderr] Adding quick-error v1.2.3 (latest: v2.0.1) [INFO] [stderr] Adding quote v0.5.2 (latest: v1.0.37) [INFO] [stderr] Adding rand v0.3.23 (latest: v0.8.5) [INFO] [stderr] Adding rand v0.4.6 (latest: v0.8.5) [INFO] [stderr] Adding rand_core v0.3.1 (latest: v0.6.4) [INFO] [stderr] Adding rand_core v0.4.2 (latest: v0.6.4) [INFO] [stderr] Adding rawpointer v0.1.0 (latest: v0.2.1) [INFO] [stderr] Adding rdrand v0.4.0 (latest: v0.8.3) [INFO] [stderr] Adding regex v0.1.80 (latest: v1.10.6) [INFO] [stderr] Adding regex v0.2.11 (latest: v1.10.6) [INFO] [stderr] Adding regex-syntax v0.3.9 (latest: v0.8.4) [INFO] [stderr] Adding regex-syntax v0.5.6 (latest: v0.8.4) [INFO] [stderr] Adding rulinalg v0.2.2 (latest: v0.4.2) [INFO] [stderr] Adding rust-htslib v0.22.0 (latest: v0.47.0) [INFO] [stderr] Adding rustc_version v0.1.7 (latest: v0.4.1) [INFO] [stderr] Adding rusty-machine v0.4.4 (latest: v0.5.4) [INFO] [stderr] Adding semver v0.1.20 (latest: v1.0.23) [INFO] [stderr] Adding statrs v0.9.0 (latest: v0.17.1) [INFO] [stderr] Adding strsim v0.8.0 (latest: v0.11.1) [INFO] [stderr] Adding textwrap v0.11.0 (latest: v0.16.1) [INFO] [stderr] Adding thread-id v2.0.0 (latest: v4.2.2) [INFO] [stderr] Adding thread_local v0.2.7 (latest: v1.1.8) [INFO] [stderr] Adding thread_local v0.3.6 (latest: v1.1.8) [INFO] [stderr] Adding time v0.1.45 (latest: v0.3.36) [INFO] [stderr] Adding ucd-util v0.1.10 (latest: v0.2.1) [INFO] [stderr] Adding unicase v1.4.2 (latest: v2.7.0) [INFO] [stderr] Adding unicode-xid v0.1.0 (latest: v0.2.5) [INFO] [stderr] Adding url v1.7.2 (latest: v2.5.2) [INFO] [stderr] Adding utf8-ranges v0.1.3 (latest: v1.0.5) [INFO] [stderr] Adding version_check v0.1.5 (latest: v0.9.5) [INFO] [stderr] Adding wasi v0.10.0+wasi-snapshot-preview1 (latest: v0.13.2+wasi-0.2.1) [INFO] [stderr] Adding which v1.0.5 (latest: v6.0.3) [INFO] [stderr] Adding winapi v0.2.8 (latest: v0.3.9) [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ab869e094a907cc5d19b4080f22eccaf347f1f95" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] warning: no edition set: defaulting to the 2015 edition while the latest is 2021 [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded num v0.1.42 [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded rulinalg v0.2.2 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded cached v0.7.0 [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded feature-probe v0.1.1 [INFO] [stderr] Downloaded c_vec v1.0.12 [INFO] [stderr] Downloaded bv v0.10.0 [INFO] [stderr] Downloaded bytecount v0.3.2 [INFO] [stderr] Downloaded itertools v0.7.11 [INFO] [stderr] Downloaded ndarray v0.6.10 [INFO] [stderr] Downloaded miniz-sys v0.1.12 [INFO] [stderr] Downloaded flate2 v0.2.20 [INFO] [stderr] Downloaded ndarray v0.12.1 [INFO] [stderr] Downloaded bindgen v0.36.1 [INFO] [stderr] Downloaded bio v0.24.0 [INFO] [stderr] Downloaded itertools v0.5.10 [INFO] [stderr] Downloaded statrs v0.9.0 [INFO] [stderr] Downloaded glob v0.2.11 [INFO] [stderr] Downloaded clang-sys v0.22.0 [INFO] [stderr] Downloaded GSL v1.1.0 [INFO] [stderr] Downloaded proc-macro2 v0.3.5 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded multimap v0.4.0 [INFO] [stderr] Downloaded fern v0.4.4 [INFO] [stderr] Downloaded cexpr v0.2.3 [INFO] [stderr] Downloaded quote v0.5.2 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded num-complex v0.1.43 [INFO] [stderr] Downloaded which v1.0.5 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded rusty-machine v0.4.4 [INFO] [stderr] Downloaded rust-htslib v0.22.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/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" "ghcr.io/rust-lang/crates-build-env/linux@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+ab869e094a907cc5d19b4080f22eccaf347f1f95" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] b5b321dea8bbc8cf865b090e3de6321e84739aa1f23d1d6eb6d5c1afb6505a8f [INFO] running `Command { std: "docker" "start" "-a" "b5b321dea8bbc8cf865b090e3de6321e84739aa1f23d1d6eb6d5c1afb6505a8f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "b5b321dea8bbc8cf865b090e3de6321e84739aa1f23d1d6eb6d5c1afb6505a8f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b5b321dea8bbc8cf865b090e3de6321e84739aa1f23d1d6eb6d5c1afb6505a8f", kill_on_drop: false }` [INFO] [stdout] b5b321dea8bbc8cf865b090e3de6321e84739aa1f23d1d6eb6d5c1afb6505a8f [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/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" "RUSTDOCFLAGS=--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" "ghcr.io/rust-lang/crates-build-env/linux@sha256:923055f121b5182466d55868a8b05e67af8ba4a3a3f6bad814e953ca3cd3ac2a" "/opt/rustwide/cargo-home/bin/cargo" "+ab869e094a907cc5d19b4080f22eccaf347f1f95" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 881a4f1f321b994889cf6d68f00dc7a4817e36fc667847b89a20c8427c0577c6 [INFO] running `Command { std: "docker" "start" "-a" "881a4f1f321b994889cf6d68f00dc7a4817e36fc667847b89a20c8427c0577c6", kill_on_drop: false }` [INFO] [stderr] warning: no edition set: defaulting to the 2015 edition while the latest is 2021 [INFO] [stderr] Compiling memchr v2.7.4 [INFO] [stderr] Compiling glob v0.2.11 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Checking rawpointer v0.1.0 [INFO] [stderr] Compiling libc v0.2.158 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling winapi-build v0.1.1 [INFO] [stderr] Compiling ucd-util v0.1.10 [INFO] [stderr] Compiling libloading v0.5.2 [INFO] [stderr] Compiling unicode-width v0.1.13 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling syn v2.0.77 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Compiling thread_local v0.3.6 [INFO] [stderr] Compiling log v0.4.22 [INFO] [stderr] Compiling humantime v1.3.0 [INFO] [stderr] Compiling proc-macro2 v0.3.5 [INFO] [stderr] Compiling kernel32-sys v0.2.2 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling regex-syntax v0.5.6 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling bitflags v1.3.2 [INFO] [stderr] Compiling ansi_term v0.12.1 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling utf8-ranges v1.0.5 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling termcolor v1.4.1 [INFO] [stderr] Compiling libz-sys v1.1.20 [INFO] [stderr] Checking log v0.3.9 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling quote v0.5.2 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Checking winapi v0.2.8 [INFO] [stderr] Compiling cfg-if v0.1.10 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling peeking_take_while v0.1.2 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling aho-corasick v0.6.10 [INFO] [stderr] Checking num-iter v0.1.45 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling version_check v0.1.5 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Checking thread-id v2.0.0 [INFO] [stderr] Checking memchr v0.1.11 [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Checking num v0.1.42 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Checking csv-core v0.1.11 [INFO] [stderr] Checking itertools v0.7.11 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking bit-vec v0.6.3 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling unicase v1.4.2 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling nom v3.2.1 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Checking bit-set v0.5.3 [INFO] [stderr] Checking rulinalg v0.2.2 [INFO] [stderr] Checking aho-corasick v0.5.3 [INFO] [stderr] Checking thread_local v0.2.7 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking statrs v0.9.0 [INFO] [stderr] Checking num-complex v0.1.43 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking ordered-float v1.1.1 [INFO] [stderr] Checking num-traits v0.1.43 [INFO] [stderr] Checking itertools v0.5.10 [INFO] [stderr] Checking itertools v0.6.5 [INFO] [stderr] Checking utf8-ranges v0.1.3 [INFO] [stderr] Checking bitflags v0.9.1 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking safemem v0.3.3 [INFO] [stderr] Checking c_vec v1.0.12 [INFO] [stderr] Compiling regex-automata v0.4.7 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Checking lazy_static v0.2.11 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking regex-syntax v0.3.9 [INFO] [stderr] Checking bytecount v0.3.2 [INFO] [stderr] Checking base64 v0.9.3 [INFO] [stderr] Checking rusty-machine v0.4.4 [INFO] [stderr] Checking mime v0.2.6 [INFO] [stderr] Checking time v0.1.45 [INFO] [stderr] Checking num_cpus v1.16.0 [INFO] [stderr] Checking traitobject v0.1.0 [INFO] [stderr] Checking regex v0.1.80 [INFO] [stderr] Checking language-tags v0.2.2 [INFO] [stderr] Checking cached v0.7.0 [INFO] [stderr] Checking typeable v0.1.2 [INFO] [stderr] Checking approx v0.1.1 [INFO] [stderr] Checking flate2 v0.2.20 [INFO] [stderr] Checking fern v0.4.4 [INFO] [stderr] Checking hyper v0.10.16 [INFO] [stderr] Checking env_logger v0.3.5 [INFO] [stderr] Compiling serde_derive v1.0.209 [INFO] [stderr] Compiling thiserror-impl v1.0.63 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Checking thiserror v1.0.63 [INFO] [stderr] Compiling regex v1.10.6 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Compiling serde v1.0.209 [INFO] [stderr] Checking csv v1.3.0 [INFO] [stderr] Checking multimap v0.4.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Compiling clap v2.34.0 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Checking libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:62:20 [INFO] [stdout] | [INFO] [stdout] 62 | let variants = try!(utils::collect_variants( [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/call/pairwise.rs:70:21 [INFO] [stdout] | [INFO] [stdout] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:75:18 [INFO] [stdout] | [INFO] [stdout] 75 | Some(try!(joint_model.pileup( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:159:26 [INFO] [stdout] | [INFO] [stdout] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/model/sample.rs:76:17 [INFO] [stdout] | [INFO] [stdout] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:62:20 [INFO] [stdout] | [INFO] [stdout] 62 | let variants = try!(utils::collect_variants( [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/call/pairwise.rs:70:21 [INFO] [stdout] | [INFO] [stdout] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:75:18 [INFO] [stdout] | [INFO] [stdout] 75 | Some(try!(joint_model.pileup( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:159:26 [INFO] [stdout] | [INFO] [stdout] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/model/sample.rs:76:17 [INFO] [stdout] | [INFO] [stdout] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `Once::new()` function is now preferred [INFO] [stdout] --> src/model/evidence/reads.rs:335:1 [INFO] [stdout] | [INFO] [stdout] 335 | / lazy_static! { [INFO] [stdout] 336 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stdout] 337 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in the macro `__lazy_static_create` which comes from the expansion of the macro `lazy_static` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `Once::new()` function is now preferred [INFO] [stdout] --> src/model/priors/single_cell_bulk.rs:26:1 [INFO] [stdout] | [INFO] [stdout] 26 | / cached! { [INFO] [stdout] 27 | | AMPLIF_CACHE: UnboundCache<(AlleleFreq, usize, usize), LogProb> = UnboundCache::new(); [INFO] [stdout] 28 | | // Lodato et al. 2015, Science, Supplementary Information, pages 8f and Fig. S5 (A, C, E) [INFO] [stdout] 29 | | // TODO: allow for non-default Lodato model parameters, e.g. learned from the data at hand [INFO] [stdout] ... | [INFO] [stdout] 96 | | } [INFO] [stdout] 97 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in the macro `__lazy_static_create` which comes from the expansion of the macro `cached` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/call/pairwise.rs:55:62 [INFO] [stdout] | [INFO] [stdout] 55 | ) -> Result>>, Box> [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: `#[warn(bare_trait_objects)]` on by default [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 55 | ) -> Result>>, Box> [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/call/pairwise.rs:116:21 [INFO] [stdout] | [INFO] [stdout] 116 | ) -> Result<(), Box> [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 116 | ) -> Result<(), Box> [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/estimation/fdr/ev.rs:35:21 [INFO] [stdout] | [INFO] [stdout] 35 | ) -> Result<(), Box> [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 35 | ) -> Result<(), Box> [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:276:35 [INFO] [stdout] | [INFO] [stdout] 276 | ) -> Result>, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 276 | ) -> Result>, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:317:21 [INFO] [stdout] | [INFO] [stdout] 317 | ) -> Result<(), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 317 | ) -> Result<(), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/reads.rs:30:49 [INFO] [stdout] | [INFO] [stdout] 30 | ) -> Result, Box>; [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 30 | ) -> Result, Box>; [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/estimation/alignment_properties.rs:40:68 [INFO] [stdout] | [INFO] [stdout] 40 | pub fn estimate(bam: &mut R) -> Result> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 40 | pub fn estimate(bam: &mut R) -> Result> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/estimation/alignment_properties.rs:142:33 [INFO] [stdout] | [INFO] [stdout] 142 | ) -> Result> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 142 | ) -> Result> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/mod.rs:275:41 [INFO] [stdout] | [INFO] [stdout] 275 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 275 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/mod.rs:416:42 [INFO] [stdout] | [INFO] [stdout] 416 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 416 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `Once::new()` function is now preferred [INFO] [stdout] --> src/model/evidence/reads.rs:335:1 [INFO] [stdout] | [INFO] [stdout] 335 | / lazy_static! { [INFO] [stdout] 336 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stdout] 337 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in the macro `__lazy_static_create` which comes from the expansion of the macro `lazy_static` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `Once::new()` function is now preferred [INFO] [stdout] --> src/model/priors/single_cell_bulk.rs:26:1 [INFO] [stdout] | [INFO] [stdout] 26 | / cached! { [INFO] [stdout] 27 | | AMPLIF_CACHE: UnboundCache<(AlleleFreq, usize, usize), LogProb> = UnboundCache::new(); [INFO] [stdout] 28 | | // Lodato et al. 2015, Science, Supplementary Information, pages 8f and Fig. S5 (A, C, E) [INFO] [stdout] 29 | | // TODO: allow for non-default Lodato model parameters, e.g. learned from the data at hand [INFO] [stdout] ... | [INFO] [stdout] 96 | | } [INFO] [stdout] 97 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in the macro `__lazy_static_create` which comes from the expansion of the macro `cached` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/fragments.rs:52:89 [INFO] [stdout] | [INFO] [stdout] 52 | pub fn estimate_insert_size(left: &bam::Record, right: &bam::Record) -> Result> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 52 | pub fn estimate_insert_size(left: &bam::Record, right: &bam::Record) -> Result> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/fragments.rs:120:41 [INFO] [stdout] | [INFO] [stdout] 120 | ) -> Result<(LogProb, LogProb), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 120 | ) -> Result<(LogProb, LogProb), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/reads.rs:56:49 [INFO] [stdout] | [INFO] [stdout] 56 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 56 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/reads.rs:101:49 [INFO] [stdout] | [INFO] [stdout] 101 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 101 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/reads.rs:169:49 [INFO] [stdout] | [INFO] [stdout] 169 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 169 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/call/pairwise.rs:55:62 [INFO] [stdout] | [INFO] [stdout] 55 | ) -> Result>>, Box> [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: `#[warn(bare_trait_objects)]` on by default [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 55 | ) -> Result>>, Box> [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/call/pairwise.rs:116:21 [INFO] [stdout] | [INFO] [stdout] 116 | ) -> Result<(), Box> [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 116 | ) -> Result<(), Box> [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/estimation/fdr/ev.rs:35:21 [INFO] [stdout] | [INFO] [stdout] 35 | ) -> Result<(), Box> [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 35 | ) -> Result<(), Box> [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:276:35 [INFO] [stdout] | [INFO] [stdout] 276 | ) -> Result>, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 276 | ) -> Result>, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:317:21 [INFO] [stdout] | [INFO] [stdout] 317 | ) -> Result<(), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 317 | ) -> Result<(), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/reads.rs:30:49 [INFO] [stdout] | [INFO] [stdout] 30 | ) -> Result, Box>; [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 30 | ) -> Result, Box>; [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/estimation/alignment_properties.rs:40:68 [INFO] [stdout] | [INFO] [stdout] 40 | pub fn estimate(bam: &mut R) -> Result> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 40 | pub fn estimate(bam: &mut R) -> Result> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/estimation/alignment_properties.rs:142:33 [INFO] [stdout] | [INFO] [stdout] 142 | ) -> Result> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 142 | ) -> Result> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/mod.rs:275:41 [INFO] [stdout] | [INFO] [stdout] 275 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 275 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/mod.rs:416:42 [INFO] [stdout] | [INFO] [stdout] 416 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 416 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:68:82 [INFO] [stdout] | [INFO] [stdout] 68 | pub fn fill(&mut self, chrom: &[u8], start: u32, end: u32) -> Result<(), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 68 | pub fn fill(&mut self, chrom: &[u8], start: u32, end: u32) -> Result<(), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:220:39 [INFO] [stdout] | [INFO] [stdout] 220 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 220 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:362:42 [INFO] [stdout] | [INFO] [stdout] 362 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 362 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:409:42 [INFO] [stdout] | [INFO] [stdout] 409 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 409 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:27:46 [INFO] [stdout] | [INFO] [stdout] 27 | ) -> Result>, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 27 | ) -> Result>, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:232:39 [INFO] [stdout] | [INFO] [stdout] 232 | ) -> Result>, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 232 | ) -> Result>, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:204:62 [INFO] [stdout] | [INFO] [stdout] 204 | pub fn seq(&mut self, chrom: &[u8]) -> Result<&[u8], Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 204 | pub fn seq(&mut self, chrom: &[u8]) -> Result<&[u8], Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:367:30 [INFO] [stdout] | [INFO] [stdout] 367 | ) -> Result> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 367 | ) -> Result> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/fragments.rs:52:89 [INFO] [stdout] | [INFO] [stdout] 52 | pub fn estimate_insert_size(left: &bam::Record, right: &bam::Record) -> Result> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 52 | pub fn estimate_insert_size(left: &bam::Record, right: &bam::Record) -> Result> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/fragments.rs:120:41 [INFO] [stdout] | [INFO] [stdout] 120 | ) -> Result<(LogProb, LogProb), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 120 | ) -> Result<(LogProb, LogProb), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/reads.rs:56:49 [INFO] [stdout] | [INFO] [stdout] 56 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 56 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/reads.rs:101:49 [INFO] [stdout] | [INFO] [stdout] 101 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 101 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/reads.rs:169:49 [INFO] [stdout] | [INFO] [stdout] 169 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 169 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:68:82 [INFO] [stdout] | [INFO] [stdout] 68 | pub fn fill(&mut self, chrom: &[u8], start: u32, end: u32) -> Result<(), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 68 | pub fn fill(&mut self, chrom: &[u8], start: u32, end: u32) -> Result<(), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:220:39 [INFO] [stdout] | [INFO] [stdout] 220 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 220 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:362:42 [INFO] [stdout] | [INFO] [stdout] 362 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 362 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:409:42 [INFO] [stdout] | [INFO] [stdout] 409 | ) -> Result, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 409 | ) -> Result, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:27:46 [INFO] [stdout] | [INFO] [stdout] 27 | ) -> Result>, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 27 | ) -> Result>, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:232:39 [INFO] [stdout] | [INFO] [stdout] 232 | ) -> Result>, Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 232 | ) -> Result>, Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:204:62 [INFO] [stdout] | [INFO] [stdout] 204 | pub fn seq(&mut self, chrom: &[u8]) -> Result<&[u8], Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 204 | pub fn seq(&mut self, chrom: &[u8]) -> Result<&[u8], Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/utils.rs:367:30 [INFO] [stdout] | [INFO] [stdout] 367 | ) -> Result> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 367 | ) -> Result> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/fragments.rs:56:68 [INFO] [stdout] | [INFO] [stdout] 56 | let aln = |rec: &bam::Record, cigar| -> Result<(u32, u32), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 56 | let aln = |rec: &bam::Record, cigar| -> Result<(u32, u32), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/evidence/fragments.rs:56:68 [INFO] [stdout] | [INFO] [stdout] 56 | let aln = |rec: &bam::Record, cigar| -> Result<(u32, u32), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 56 | let aln = |rec: &bam::Record, cigar| -> Result<(u32, u32), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:363:34 [INFO] [stdout] | [INFO] [stdout] 363 | let mut evidence: RefMut = match variant { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 363 | let mut evidence: RefMut = match variant { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:412:44 [INFO] [stdout] | [INFO] [stdout] 412 | -> Result<(LogProb, LogProb), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 412 | -> Result<(LogProb, LogProb), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:363:34 [INFO] [stdout] | [INFO] [stdout] 363 | let mut evidence: RefMut = match variant { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 363 | let mut evidence: RefMut = match variant { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/model/sample.rs:412:44 [INFO] [stdout] | [INFO] [stdout] 412 | -> Result<(LogProb, LogProb), Box> { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] help: if this is an object-safe trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 412 | -> Result<(LogProb, LogProb), Box> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 33 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this method call resolves to `<&[T; N] as IntoIterator>::into_iter` (due to backwards compatibility), but will resolve to `<[T; N] as IntoIterator>::into_iter` in Rust 2021 [INFO] [stdout] --> src/model/sample.rs:612:79 [INFO] [stdout] | [INFO] [stdout] 612 | for (record, true_alt_prob) in records.into_iter().zip(true_alt_probs.into_iter()) { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this changes meaning in Rust 2021 [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: `#[warn(array_into_iter)]` on by default [INFO] [stdout] help: use `.iter()` instead of `.into_iter()` to avoid ambiguity [INFO] [stdout] | [INFO] [stdout] 612 | for (record, true_alt_prob) in records.into_iter().zip(true_alt_probs.iter()) { [INFO] [stdout] | ~~~~ [INFO] [stdout] help: or use `IntoIterator::into_iter(..)` instead of `.into_iter()` to explicitly iterate by value [INFO] [stdout] | [INFO] [stdout] 612 | for (record, true_alt_prob) in records.into_iter().zip(IntoIterator::into_iter(true_alt_probs)) { [INFO] [stdout] | ++++++++++++++++++++++++ ~ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 34 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 42.25s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nom v3.2.1, traitobject v0.1.0 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 3` [INFO] running `Command { std: "docker" "inspect" "881a4f1f321b994889cf6d68f00dc7a4817e36fc667847b89a20c8427c0577c6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "881a4f1f321b994889cf6d68f00dc7a4817e36fc667847b89a20c8427c0577c6", kill_on_drop: false }` [INFO] [stdout] 881a4f1f321b994889cf6d68f00dc7a4817e36fc667847b89a20c8427c0577c6