[INFO] fetching crate libprosic 0.7.3... [INFO] testing libprosic-0.7.3 against master#62efba8a050c64249dab942951bb28f710208bc8 for pr-90799 [INFO] extracting crate libprosic 0.7.3 into /workspace/builds/worker-95/source [INFO] validating manifest of crates.io crate libprosic 0.7.3 on toolchain 62efba8a050c64249dab942951bb28f710208bc8 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "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-95/source/Cargo.toml [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-95/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-95/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:e8397a04204aaf8b9f284182a6f9e27a3c2e67044d0943b4415b160bfc957681" "/opt/rustwide/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 2ea9465de5327330965196b3cfd51609b16980e1b6876de939f36c88be2e6c73 [INFO] running `Command { std: "docker" "start" "-a" "2ea9465de5327330965196b3cfd51609b16980e1b6876de939f36c88be2e6c73", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "2ea9465de5327330965196b3cfd51609b16980e1b6876de939f36c88be2e6c73", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "2ea9465de5327330965196b3cfd51609b16980e1b6876de939f36c88be2e6c73", kill_on_drop: false }` [INFO] [stdout] 2ea9465de5327330965196b3cfd51609b16980e1b6876de939f36c88be2e6c73 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-95/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-95/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" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e8397a04204aaf8b9f284182a6f9e27a3c2e67044d0943b4415b160bfc957681" "/opt/rustwide/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 48459cfe506bbcd4ae870f4520b035a95fda932303ae2588d12468dc2638410c [INFO] running `Command { std: "docker" "start" "-a" "48459cfe506bbcd4ae870f4520b035a95fda932303ae2588d12468dc2638410c", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling libc v0.2.108 [INFO] [stderr] Compiling proc-macro2 v1.0.32 [INFO] [stderr] Compiling unicode-xid v0.2.2 [INFO] [stderr] Compiling syn v1.0.82 [INFO] [stderr] Compiling cc v1.0.72 [INFO] [stderr] Compiling serde_derive v1.0.130 [INFO] [stderr] Compiling pkg-config v0.3.22 [INFO] [stderr] Compiling serde v1.0.130 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling either v1.6.1 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling rustversion v1.0.5 [INFO] [stderr] Compiling ucd-util v0.1.8 [INFO] [stderr] Compiling rawpointer v0.1.0 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling unicode-segmentation v1.8.0 [INFO] [stderr] Compiling bitflags v1.3.2 [INFO] [stderr] Compiling tinyvec_macros v0.1.0 [INFO] [stderr] Compiling utf8-ranges v1.0.4 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling ryu v1.0.6 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling regex-automata v0.1.10 [INFO] [stderr] Compiling matches v0.1.9 [INFO] [stderr] Compiling unicode-bidi v0.3.7 [INFO] [stderr] Compiling bit-vec v0.6.3 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling itoa v0.4.8 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling byteorder v1.4.3 [INFO] [stderr] Compiling percent-encoding v1.0.1 [INFO] [stderr] Compiling bitflags v0.9.1 [INFO] [stderr] Compiling fnv v1.0.7 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling c_vec v1.0.12 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling lazy_static v0.2.11 [INFO] [stderr] Compiling approx v0.1.1 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling thread_local v0.3.6 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling aho-corasick v0.6.10 [INFO] [stderr] Compiling csv-core v0.1.10 [INFO] [stderr] Compiling proc-macro2 v0.3.5 [INFO] [stderr] Compiling regex-syntax v0.5.6 [INFO] [stderr] Compiling itertools v0.7.11 [INFO] [stderr] Compiling itertools v0.6.5 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling tinyvec v1.5.1 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling bit-set v0.5.2 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling heck v0.3.3 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling num-iter v0.1.42 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling quote v0.5.2 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling libloading v0.5.2 [INFO] [stderr] Compiling libz-sys v1.1.3 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Compiling rand v0.4.6 [INFO] [stderr] Compiling quote v1.0.10 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling nom v3.2.1 [INFO] [stderr] Compiling unicode-normalization v0.1.19 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling num-traits v0.1.43 [INFO] [stderr] Compiling ordered-float v1.1.1 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling rand v0.3.23 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling num v0.1.42 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Compiling idna v0.1.5 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling url v1.7.2 [INFO] [stderr] Compiling thiserror-impl v1.0.30 [INFO] [stderr] Compiling strum_macros v0.23.1 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling thiserror v1.0.30 [INFO] [stderr] Compiling bio-types v0.12.1 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling bstr v0.2.17 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling clap v2.34.0 [INFO] [stderr] Compiling csv v1.1.6 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [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] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(bare_trait_objects)]` on by default [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] [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: 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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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: 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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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: 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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn evidence::reads::AbstractReadEvidence` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `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` (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 `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` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 33 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 51.12s [INFO] running `Command { std: "docker" "inspect" "48459cfe506bbcd4ae870f4520b035a95fda932303ae2588d12468dc2638410c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "48459cfe506bbcd4ae870f4520b035a95fda932303ae2588d12468dc2638410c", kill_on_drop: false }` [INFO] [stdout] 48459cfe506bbcd4ae870f4520b035a95fda932303ae2588d12468dc2638410c [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-95/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-95/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" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e8397a04204aaf8b9f284182a6f9e27a3c2e67044d0943b4415b160bfc957681" "/opt/rustwide/cargo-home/bin/cargo" "+62efba8a050c64249dab942951bb28f710208bc8" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 8ee2d1d3e2428f92b18cf3351b8ea2641e14578ab416f1c01e5cd31c1366e257 [INFO] running `Command { std: "docker" "start" "-a" "8ee2d1d3e2428f92b18cf3351b8ea2641e14578ab416f1c01e5cd31c1366e257", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling winapi-build v0.1.1 [INFO] [stderr] Compiling winapi v0.2.8 [INFO] [stderr] Compiling version_check v0.1.5 [INFO] [stderr] Compiling httparse v1.5.1 [INFO] [stderr] Compiling regex-syntax v0.3.9 [INFO] [stderr] Compiling utf8-ranges v0.1.3 [INFO] [stderr] Compiling safemem v0.3.3 [INFO] [stderr] Compiling typeable v0.1.2 [INFO] [stderr] Compiling traitobject v0.1.0 [INFO] [stderr] Compiling language-tags v0.2.2 [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling memchr v0.1.11 [INFO] [stderr] Compiling time v0.1.44 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling mime v0.2.6 [INFO] [stderr] Compiling fern v0.4.4 [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] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(bare_trait_objects)]` on by default [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] [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: 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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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: 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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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: 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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn evidence::reads::AbstractReadEvidence` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `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` (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 `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` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 33 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling aho-corasick v0.5.3 [INFO] [stderr] Compiling kernel32-sys v0.2.2 [INFO] [stderr] Compiling base64 v0.9.3 [INFO] [stderr] Compiling unicase v1.4.2 [INFO] [stderr] Compiling thread-id v2.0.0 [INFO] [stderr] Compiling thread_local v0.2.7 [INFO] [stderr] Compiling hyper v0.10.16 [INFO] [stderr] Compiling regex v0.1.80 [INFO] [stderr] Compiling flate2 v0.2.20 [INFO] [stderr] Compiling env_logger v0.3.5 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [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] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(bare_trait_objects)]` on by default [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] [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: 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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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: 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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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: 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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn evidence::reads::AbstractReadEvidence` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] | ^^^^^ help: use `dyn`: `dyn Error` [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] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `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` (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 `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` (in Nightly builds, run with -Z macro-backtrace for more info) [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] = note: `#[warn(array_into_iter)]` on by default [INFO] [stdout] = warning: this changes meaning in Rust 2021 [INFO] [stdout] = note: for more information, see [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] [ERROR] error running command: no output for 300 seconds [INFO] running `Command { std: "docker" "inspect" "8ee2d1d3e2428f92b18cf3351b8ea2641e14578ab416f1c01e5cd31c1366e257", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8ee2d1d3e2428f92b18cf3351b8ea2641e14578ab416f1c01e5cd31c1366e257", kill_on_drop: false }` [INFO] [stdout] 8ee2d1d3e2428f92b18cf3351b8ea2641e14578ab416f1c01e5cd31c1366e257