[INFO] fetching crate libprosic 0.7.3... [INFO] testing libprosic-0.7.3 against beta-2021-01-01 for beta-1.50-1 [INFO] extracting crate libprosic 0.7.3 into /workspace/builds/worker-1/source [INFO] validating manifest of crates.io crate libprosic 0.7.3 on toolchain beta-2021-01-01 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2021-01-01" "read-manifest" "--manifest-path" "Cargo.toml", 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-1/source/Cargo.toml [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2021-01-01" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }` [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2021-01-01" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded feature-probe v0.1.1 [INFO] [stderr] Downloaded bio-types v0.7.0 [INFO] [stderr] Downloaded statrs v0.9.0 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded c_vec v1.0.12 [INFO] [stderr] Downloaded cached v0.7.0 [INFO] [stderr] Downloaded bv v0.10.0 [INFO] [stderr] Downloaded rusty-machine v0.4.4 [INFO] [stderr] Downloaded rulinalg v0.2.2 [INFO] [stderr] Downloaded ndarray v0.6.10 [INFO] [stderr] Downloaded bio v0.24.0 [INFO] [stderr] Downloaded GSL v1.1.0 [INFO] [stderr] Downloaded rust-htslib v0.22.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:b8eeb62f26c39b23691079a6cb6de528d8e88b4d71a8f6b1d30f8ba7d9c16de9" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-01-01" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 93fcc92e04decdedcf9f22c2cb90ad413f6d836a00e52217f0472395085345a6 [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "93fcc92e04decdedcf9f22c2cb90ad413f6d836a00e52217f0472395085345a6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "93fcc92e04decdedcf9f22c2cb90ad413f6d836a00e52217f0472395085345a6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "93fcc92e04decdedcf9f22c2cb90ad413f6d836a00e52217f0472395085345a6", kill_on_drop: false }` [INFO] [stdout] 93fcc92e04decdedcf9f22c2cb90ad413f6d836a00e52217f0472395085345a6 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:b8eeb62f26c39b23691079a6cb6de528d8e88b4d71a8f6b1d30f8ba7d9c16de9" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-01-01" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 49480da35059990a0b0a3fbd6fde5d77a5edbd588df0614eafe4e8899c8f73c8 [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "49480da35059990a0b0a3fbd6fde5d77a5edbd588df0614eafe4e8899c8f73c8", kill_on_drop: false }` [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling rawpointer v0.1.0 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling c_vec v1.0.12 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling proc-macro2 v0.3.5 [INFO] [stderr] Compiling itertools v0.6.5 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling rand v0.3.23 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling bstr v0.2.14 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling quote v0.5.2 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling csv v1.1.5 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling bio-types v0.7.0 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Compiling 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: 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] [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/call/pairwise.rs:116:21 [INFO] [stdout] | [INFO] [stdout] 116 | ) -> Result<(), Box> [INFO] [stdout] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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: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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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 a macro (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 a macro (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 39.82s [INFO] running `Command { std: "docker" "inspect" "49480da35059990a0b0a3fbd6fde5d77a5edbd588df0614eafe4e8899c8f73c8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "49480da35059990a0b0a3fbd6fde5d77a5edbd588df0614eafe4e8899c8f73c8", kill_on_drop: false }` [INFO] [stdout] 49480da35059990a0b0a3fbd6fde5d77a5edbd588df0614eafe4e8899c8f73c8 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:b8eeb62f26c39b23691079a6cb6de528d8e88b4d71a8f6b1d30f8ba7d9c16de9" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-01-01" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 8598c217c3d4d67e1cbc16e3fd62b4be2504f7639c2e99687d58bb6d37f2c79c [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "8598c217c3d4d67e1cbc16e3fd62b4be2504f7639c2e99687d58bb6d37f2c79c", kill_on_drop: false }` [INFO] [stderr] Compiling memchr v0.1.11 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] Compiling thread-id v2.0.0 [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: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] [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/call/pairwise.rs:116:21 [INFO] [stdout] | [INFO] [stdout] 116 | ) -> Result<(), Box> [INFO] [stdout] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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: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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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 a macro (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 a macro (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 thread_local v0.2.7 [INFO] [stderr] Compiling flate2 v0.2.20 [INFO] [stderr] Compiling aho-corasick v0.5.3 [INFO] [stderr] Compiling hyper v0.10.16 [INFO] [stderr] Compiling regex v0.1.80 [INFO] [stderr] Compiling env_logger v0.3.5 [INFO] [stderr] Compiling 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: 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] [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/call/pairwise.rs:116:21 [INFO] [stdout] | [INFO] [stdout] 116 | ) -> Result<(), Box> [INFO] [stdout] | ^^^^^ help: use `dyn`: `dyn Error` [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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: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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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] [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 a macro (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 a macro (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this method call currently resolves to `<&[T; N] as IntoIterator>::into_iter` (due to autoref coercions), but that might change in the future when `IntoIterator` impls for arrays are added. [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] | ^^^^^^^^^ help: use `.iter()` instead of `.into_iter()` to avoid ambiguity: `iter` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(array_into_iter)]` on by default [INFO] [stdout] = warning: this was previously accepted by the compiler but is being phased out; it will become a hard error in a future release! [INFO] [stdout] = note: for more information, see issue #66145 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: linking with `cc` failed: exit code: 1 [INFO] [stdout] | [INFO] [stdout] = note: "cc" "-Wl,--as-needed" "-Wl,-z,noexecstack" "-m64" "-Wl,--eh-frame-hdr" "-L" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.0.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.1.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.10.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.11.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.12.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.13.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.14.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.15.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.2.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.3.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.4.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.5.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.6.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.7.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.8.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.libprosic.cblx9q58-cgu.9.rcgu.o" "-o" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5" "/opt/rustwide/target/debug/deps/libprosic-0ca9c6a8bfe9dde5.kue6thweceezsbp.rcgu.o" "-Wl,--gc-sections" "-pie" "-Wl,-zrelro" "-Wl,-znow" "-nodefaultlibs" "-L" "/opt/rustwide/target/debug/deps" "-L" "/opt/rustwide/target/debug/build/miniz-sys-afed702fff7fb987/out" "-L" "/opt/rustwide/target/debug/build/rust-htslib-2063ca52c9494882/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-d46d26621a646e0b/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libtest-c99ebba9851136ef.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libterm-190ecd0479955c2e.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgetopts-10cf7eacb763a707.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunicode_width-5f0069e1a0595222.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_std-176a753cf8833059.rlib" "/opt/rustwide/target/debug/deps/libenv_logger-a760d1db56e931d3.rlib" "/opt/rustwide/target/debug/deps/libregex-5cf5115af643379c.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-d1a635b7c3059b5b.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-733e611f959c7336.rlib" "/opt/rustwide/target/debug/deps/libthread_local-beacca994da825ed.rlib" "/opt/rustwide/target/debug/deps/libthread_id-e3d810dfd6892b0d.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-6d6d4dc291ffa3c7.rlib" "/opt/rustwide/target/debug/deps/libmemchr-70509d288bbc3136.rlib" "/opt/rustwide/target/debug/deps/libcached-832bf67640b8fb59.rlib" "/opt/rustwide/target/debug/deps/libregex-e9469c13a0c9458c.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-5f7e849363b8b7b2.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-7cceea5d5695388b.rlib" "/opt/rustwide/target/debug/deps/libucd_util-91926941ec642f05.rlib" "/opt/rustwide/target/debug/deps/libthread_local-812f6a3f0004ea44.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-abfc7d224a5da1ac.rlib" "/opt/rustwide/target/debug/deps/librusty_machine-7a8a9c7504c810f6.rlib" "/opt/rustwide/target/debug/deps/librulinalg-b494014db2da14de.rlib" "/opt/rustwide/target/debug/deps/libnum-74cbb70d611c8948.rlib" "/opt/rustwide/target/debug/deps/libnum_iter-aa130faf49ab8f05.rlib" "/opt/rustwide/target/debug/deps/libndarray-d78579f17deb410c.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-c2be7d7ce8e6c21b.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-ce76a0740b185d80.rlib" "/opt/rustwide/target/debug/deps/libitertools-53848a55d364ffd2.rlib" "/opt/rustwide/target/debug/deps/libapprox-b4df0ddee91d9b37.rlib" "/opt/rustwide/target/debug/deps/librgsl-674a809a31bc108d.rlib" "/opt/rustwide/target/debug/deps/libc_vec-fd1b2b07c21ad0f0.rlib" "/opt/rustwide/target/debug/deps/liblog-2151a70b73779053.rlib" "/opt/rustwide/target/debug/deps/liblog-93afe3d9087c158b.rlib" "/opt/rustwide/target/debug/deps/libcfg_if-3bb9a546b52233f2.rlib" "/opt/rustwide/target/debug/deps/librust_htslib-4664d32ee7a683ff.rlib" "/opt/rustwide/target/debug/deps/liblzma_sys-b91c224a570c857e.rlib" "/opt/rustwide/target/debug/deps/libbzip2_sys-0bd64e2572705ac2.rlib" "/opt/rustwide/target/debug/deps/liblibz_sys-81fc3e20f4ab8332.rlib" "/opt/rustwide/target/debug/deps/liblinear_map-2a53e5f1cf43edbb.rlib" "/opt/rustwide/target/debug/deps/liburl-c133a665db6f3586.rlib" "/opt/rustwide/target/debug/deps/libpercent_encoding-a1c8d337a4da41fd.rlib" "/opt/rustwide/target/debug/deps/libidna-05ee6e9e5693c264.rlib" "/opt/rustwide/target/debug/deps/libunicode_normalization-7468a419cdf9d732.rlib" "/opt/rustwide/target/debug/deps/libtinyvec-9737c6d444d5d4fb.rlib" "/opt/rustwide/target/debug/deps/libtinyvec_macros-fd04830c7eee2552.rlib" "/opt/rustwide/target/debug/deps/libunicode_bidi-2a3427138786ef48.rlib" "/opt/rustwide/target/debug/deps/libmatches-48febceb3dcc9296.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-721ddb5cf32cc140.rlib" "/opt/rustwide/target/debug/deps/libitertools-2d69cd3dd928321d.rlib" "/opt/rustwide/target/debug/deps/libieee754-f0c46de161a21699.rlib" "/opt/rustwide/target/debug/deps/libbitflags-244aa335565f38bd.rlib" "/opt/rustwide/target/debug/deps/libbio-a4a5a2b9b2336cf7.rlib" "/opt/rustwide/target/debug/deps/libfxhash-c2bd72848bedb4c6.rlib" "/opt/rustwide/target/debug/deps/libvec_map-94884dbc81c5b611.rlib" "/opt/rustwide/target/debug/deps/libstatrs-65a515269773837d.rlib" "/opt/rustwide/target/debug/deps/librand-1e6d27f56d1fe794.rlib" "/opt/rustwide/target/debug/deps/librand-ffff075fe818a88b.rlib" "/opt/rustwide/target/debug/deps/liblibc-9989f552ab23e563.rlib" "/opt/rustwide/target/debug/deps/libfnv-9bab2cd4d16544dd.rlib" "/opt/rustwide/target/debug/deps/libbv-85c5fd467a835d35.rlib" "/opt/rustwide/target/debug/deps/libordered_float-2a13246c91d262b3.rlib" "/opt/rustwide/target/debug/deps/libnum_integer-d35afb76f1c5386c.rlib" "/opt/rustwide/target/debug/deps/libnewtype_derive-4d7db816894fb59f.rlib" "/opt/rustwide/target/debug/deps/libndarray-c1fe5c8385f49633.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-ce78ac30a93fc2b0.rlib" "/opt/rustwide/target/debug/deps/libmatrixmultiply-51ef73fd4bc3277c.rlib" "/opt/rustwide/target/debug/deps/librawpointer-d277d1333570e91b.rlib" "/opt/rustwide/target/debug/deps/libmultimap-27d4d8fb9d4339ce.rlib" "/opt/rustwide/target/debug/deps/libitertools_num-d9d371f784886064.rlib" "/opt/rustwide/target/debug/deps/libitertools-277e9a446fdb6c8d.rlib" "/opt/rustwide/target/debug/deps/libeither-253b1295061796dc.rlib" "/opt/rustwide/target/debug/deps/libcustom_derive-2e93790494c48e84.rlib" "/opt/rustwide/target/debug/deps/libcsv-e9bcd1a84560df78.rlib" "/opt/rustwide/target/debug/deps/libryu-f21f59bb2c528cca.rlib" "/opt/rustwide/target/debug/deps/libitoa-7705fc0f005bae91.rlib" "/opt/rustwide/target/debug/deps/libcsv_core-bce3f2882fada0e9.rlib" "/opt/rustwide/target/debug/deps/libbstr-f9aeb623433f9066.rlib" "/opt/rustwide/target/debug/deps/libregex_automata-8f0355b2276acf56.rlib" "/opt/rustwide/target/debug/deps/libbyteorder-2f9d4a3f19411b1e.rlib" "/opt/rustwide/target/debug/deps/libbytecount-9a0178f602bb44b9.rlib" "/opt/rustwide/target/debug/deps/libbit_set-b558fc6c0c493de5.rlib" "/opt/rustwide/target/debug/deps/libbit_vec-3f19f205a477929d.rlib" "/opt/rustwide/target/debug/deps/libapprox-fe40064de4c3b6e2.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-cb2b583837c7ff21.rlib" "/opt/rustwide/target/debug/deps/libbio_types-93d971d74c7b7d2c.rlib" "/opt/rustwide/target/debug/deps/libserde-2a7155d8267aab02.rlib" "/opt/rustwide/target/debug/deps/libregex-88a1e75c7e2bfbce.rlib" "/opt/rustwide/target/debug/deps/libthread_local-abd19461110d9879.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-2e7c3a315d0632c2.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-d0ef70c30ec66613.rlib" "/opt/rustwide/target/debug/deps/libmemchr-e5604f0874edb5fe.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-b2d06f7d60fcbb27.rlib" "/opt/rustwide/target/debug/deps/libquick_error-671ab0df75bdceb5.rlib" "-Wl,--start-group" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-7444fd17919e9af0.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-0ee2f67026959ab7.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libminiz_oxide-df1bcd1e82256d04.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libadler-ed9ecf1b54021131.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libobject-0ede66bb24e94b96.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libaddr2line-7c2de7f50940865c.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgimli-b138d50085fd4683.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-6576870d8f2b9ae2.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-042a30c5f67b2c91.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-7b3f33d3dbe385dc.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-90b3063cd7b22527.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-17f9484f8dc4da1e.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-df38345acd9d92e1.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-a5e10ca10bdd9e54.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-9e5b4162eeef2cef.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-3a4e739a77468800.rlib" "-Wl,--end-group" "/opt/rustwide/rustup-home/toolchains/beta-2021-01-01-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-0f3a0c116d5e04d6.rlib" "-Wl,-Bdynamic" "-llzma" "-lz" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" [INFO] [stdout] = note: /usr/bin/ld: /opt/rustwide/target/debug/deps/librgsl-674a809a31bc108d.rlib(rgsl-674a809a31bc108d.rgsl.7088rd7d-cgu.10.rcgu.o): in function `rgsl::randist::gaussian::gaussian_pdf': [INFO] [stdout] /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/randist/gaussian.rs:20: undefined reference to `gsl_ran_gaussian_pdf' [INFO] [stdout] /usr/bin/ld: /opt/rustwide/target/debug/deps/librgsl-674a809a31bc108d.rlib(rgsl-674a809a31bc108d.rgsl.7088rd7d-cgu.10.rcgu.o): in function `rgsl::randist::gaussian::ugaussian_P': [INFO] [stdout] /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/randist/gaussian.rs:73: undefined reference to `gsl_cdf_ugaussian_P' [INFO] [stdout] /usr/bin/ld: /opt/rustwide/target/debug/deps/librgsl-674a809a31bc108d.rlib(rgsl-674a809a31bc108d.rgsl.7088rd7d-cgu.8.rcgu.o): in function `rgsl::error::erfc': [INFO] [stdout] /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/error.rs:28: undefined reference to `gsl_sf_erfc' [INFO] [stdout] collect2: error: ld returned 1 exit status [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to previous error; 34 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `libprosic` [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [INFO] running `Command { std: "docker" "inspect" "8598c217c3d4d67e1cbc16e3fd62b4be2504f7639c2e99687d58bb6d37f2c79c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8598c217c3d4d67e1cbc16e3fd62b4be2504f7639c2e99687d58bb6d37f2c79c", kill_on_drop: false }` [INFO] [stdout] 8598c217c3d4d67e1cbc16e3fd62b4be2504f7639c2e99687d58bb6d37f2c79c