[INFO] crate libprosic 0.7.3 is already in cache [INFO] testing libprosic-0.7.3 against beta-2020-07-24 for beta-1.46-1 [INFO] extracting crate libprosic 0.7.3 into /workspace/builds/worker-5/source [INFO] validating manifest of crates.io crate libprosic 0.7.3 on toolchain beta-2020-07-24 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-07-24" "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-5/source/Cargo.toml [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-07-24" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }` [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2020-07-24" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env@sha256:a636fd89d022f18117e1dc8fb37a0a009933cdbbe082814857f0e2024962d47c" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-07-24" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 806ad8e5d7cc0f3989298f1aa00016f7aa82813a5753d27718cf02bcedc9faaa [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" "806ad8e5d7cc0f3989298f1aa00016f7aa82813a5753d27718cf02bcedc9faaa", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "806ad8e5d7cc0f3989298f1aa00016f7aa82813a5753d27718cf02bcedc9faaa", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "806ad8e5d7cc0f3989298f1aa00016f7aa82813a5753d27718cf02bcedc9faaa", kill_on_drop: false }` [INFO] [stdout] 806ad8e5d7cc0f3989298f1aa00016f7aa82813a5753d27718cf02bcedc9faaa [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env@sha256:a636fd89d022f18117e1dc8fb37a0a009933cdbbe082814857f0e2024962d47c" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-07-24" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 986bd471ef728b97d4f40bd94755e7c3b18772e26d0c051184033076e49ae4cb [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" "986bd471ef728b97d4f40bd94755e7c3b18772e26d0c051184033076e49ae4cb", kill_on_drop: false }` [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 ndarray v0.6.10 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling bit-vec v0.6.2 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling c_vec v1.0.12 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling approx v0.1.1 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling lzma-sys v0.1.16 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling proc-macro2 v0.3.5 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling csv-core v0.1.10 [INFO] [stderr] Compiling rand v0.4.6 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling ordered-float v1.1.0 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling bit-set v0.5.2 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling quote v0.5.2 [INFO] [stderr] Compiling num v0.1.42 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling bstr v0.2.13 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling rand v0.3.23 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling clap v2.33.2 [INFO] [stderr] Compiling bio-types v0.7.0 [INFO] [stderr] Compiling csv v1.1.3 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stdout] warning: use of deprecated item '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 item '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 item 'try': use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:75:18 [INFO] [stdout] | [INFO] [stdout] 75 | Some(try!(joint_model.pileup( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:159:26 [INFO] [stdout] | [INFO] [stdout] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated item '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/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: 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: 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 item '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 item '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 58.43s [INFO] running `Command { std: "docker" "inspect" "986bd471ef728b97d4f40bd94755e7c3b18772e26d0c051184033076e49ae4cb", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "986bd471ef728b97d4f40bd94755e7c3b18772e26d0c051184033076e49ae4cb", kill_on_drop: false }` [INFO] [stdout] 986bd471ef728b97d4f40bd94755e7c3b18772e26d0c051184033076e49ae4cb [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env@sha256:a636fd89d022f18117e1dc8fb37a0a009933cdbbe082814857f0e2024962d47c" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-07-24" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 3d35ca507199d7d4628a813fe5ab92170b5fce693c8d155d7000e4ea96ebb737 [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" "3d35ca507199d7d4628a813fe5ab92170b5fce693c8d155d7000e4ea96ebb737", kill_on_drop: false }` [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling memchr v0.1.11 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling thread-id v2.0.0 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stdout] warning: use of deprecated item '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 item '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 item 'try': use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:75:18 [INFO] [stdout] | [INFO] [stdout] 75 | Some(try!(joint_model.pileup( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:159:26 [INFO] [stdout] | [INFO] [stdout] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated item '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/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: 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: 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 item '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 item '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 hyper v0.10.16 [INFO] [stderr] Compiling aho-corasick v0.5.3 [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: use of deprecated item '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 item '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 item 'try': use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:75:18 [INFO] [stdout] | [INFO] [stdout] 75 | Some(try!(joint_model.pileup( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:159:26 [INFO] [stdout] | [INFO] [stdout] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated item '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/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: 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: 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 item '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 item '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-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.0.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.1.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.10.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.11.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.12.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.13.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.14.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.15.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.2.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.3.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.4.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.5.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.6.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.7.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.8.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.libprosic.7nj15jxz-cgu.9.rcgu.o" "-o" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b" "/opt/rustwide/target/debug/deps/libprosic-ef66dcdac242160b.3g4mwcdnrwa64uab.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-9ee67057a79cd42e/out" "-L" "/opt/rustwide/target/debug/build/rust-htslib-ee44505948b5514d/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-4d88153c5a8d9249/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libtest-12320b97c89568cd.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libterm-700356192fffd298.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgetopts-b7642fe67be89b55.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunicode_width-5281c8ee01ffdf7b.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_std-a4e3948fb2172e36.rlib" "/opt/rustwide/target/debug/deps/libenv_logger-f170f1cfb842e995.rlib" "/opt/rustwide/target/debug/deps/libregex-3fb3ee4a1f92650e.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-84ed10061b506991.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-63e7e7ed077eef28.rlib" "/opt/rustwide/target/debug/deps/libthread_local-85fedaa7d28acda1.rlib" "/opt/rustwide/target/debug/deps/libthread_id-a521b78f9b31033a.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-52729487435fe106.rlib" "/opt/rustwide/target/debug/deps/libmemchr-935c83ca5376e130.rlib" "/opt/rustwide/target/debug/deps/libcached-f83499e9df0057d5.rlib" "/opt/rustwide/target/debug/deps/libregex-905b8d3206476f39.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-be40cb5dc3f0ecb6.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-5ac0967dc3296fed.rlib" "/opt/rustwide/target/debug/deps/libucd_util-84c9c8f4a23971c2.rlib" "/opt/rustwide/target/debug/deps/libthread_local-5aeca77422c2c02a.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-bf56872a80c7637d.rlib" "/opt/rustwide/target/debug/deps/librusty_machine-7dd3406b881c569c.rlib" "/opt/rustwide/target/debug/deps/librulinalg-94688c6786c915c6.rlib" "/opt/rustwide/target/debug/deps/libnum-9b57e9962057c6cd.rlib" "/opt/rustwide/target/debug/deps/libnum_iter-6656b01f45368b3a.rlib" "/opt/rustwide/target/debug/deps/libndarray-668cb404e24c5041.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-434454653e314e7c.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-7c88e41e0e7adede.rlib" "/opt/rustwide/target/debug/deps/libitertools-7ca89af2d4546bd1.rlib" "/opt/rustwide/target/debug/deps/libapprox-43cd5c53f5296d66.rlib" "/opt/rustwide/target/debug/deps/librgsl-77eeeaa41aab4217.rlib" "/opt/rustwide/target/debug/deps/libc_vec-287aaf910ec28e78.rlib" "/opt/rustwide/target/debug/deps/liblog-61b6b7789e2ddc7f.rlib" "/opt/rustwide/target/debug/deps/liblog-51760c8d9f0a0b95.rlib" "/opt/rustwide/target/debug/deps/libcfg_if-727e218cbe4629d5.rlib" "/opt/rustwide/target/debug/deps/librust_htslib-ceef00ecf091a45a.rlib" "/opt/rustwide/target/debug/deps/liblzma_sys-0d2c7c8276eee947.rlib" "/opt/rustwide/target/debug/deps/libbzip2_sys-bea7e668af695ace.rlib" "/opt/rustwide/target/debug/deps/liblibz_sys-82a17464aa03e971.rlib" "/opt/rustwide/target/debug/deps/liblinear_map-b61e5b71d4892b74.rlib" "/opt/rustwide/target/debug/deps/liburl-fe1a89f05a35db1f.rlib" "/opt/rustwide/target/debug/deps/libpercent_encoding-88e6a83f9628f22c.rlib" "/opt/rustwide/target/debug/deps/libidna-9b3f5f4a98c2524e.rlib" "/opt/rustwide/target/debug/deps/libunicode_normalization-5396cea98cf3fbab.rlib" "/opt/rustwide/target/debug/deps/libtinyvec-0ac8f90e9b502e48.rlib" "/opt/rustwide/target/debug/deps/libunicode_bidi-378825f0a341ccf9.rlib" "/opt/rustwide/target/debug/deps/libmatches-bbcc1f6f6a0b4874.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-2ea69cae54b65af6.rlib" "/opt/rustwide/target/debug/deps/libitertools-bb12dfc8081b0f25.rlib" "/opt/rustwide/target/debug/deps/libieee754-835eb73baa575f73.rlib" "/opt/rustwide/target/debug/deps/libbitflags-e1adf2d5a3c5eab4.rlib" "/opt/rustwide/target/debug/deps/libbio-873a8aaeb5469f41.rlib" "/opt/rustwide/target/debug/deps/libfxhash-bc35a5da7240a59b.rlib" "/opt/rustwide/target/debug/deps/libvec_map-c851add392e7ef19.rlib" "/opt/rustwide/target/debug/deps/libstatrs-8ab5b27e2e03fd67.rlib" "/opt/rustwide/target/debug/deps/librand-324bdf42a0f1fa7c.rlib" "/opt/rustwide/target/debug/deps/librand-1cbb718ef3c1411b.rlib" "/opt/rustwide/target/debug/deps/liblibc-45a30d68be4460eb.rlib" "/opt/rustwide/target/debug/deps/libfnv-c2227cfbdd7b9572.rlib" "/opt/rustwide/target/debug/deps/libbv-b8d60de65f799344.rlib" "/opt/rustwide/target/debug/deps/libordered_float-e1661aa7bb0c88ac.rlib" "/opt/rustwide/target/debug/deps/libnum_integer-94fd0f13cfea77ad.rlib" "/opt/rustwide/target/debug/deps/libnewtype_derive-133977346bd0001a.rlib" "/opt/rustwide/target/debug/deps/libndarray-f091f40529cffc39.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-dfe6abfbbeea45ff.rlib" "/opt/rustwide/target/debug/deps/libmatrixmultiply-62b42c300a06e887.rlib" "/opt/rustwide/target/debug/deps/librawpointer-6e70b81014f9f8f5.rlib" "/opt/rustwide/target/debug/deps/libmultimap-14d65a6e66f9042d.rlib" "/opt/rustwide/target/debug/deps/libitertools_num-6b7eb972d7fc9102.rlib" "/opt/rustwide/target/debug/deps/libitertools-3bcfd319e8a7b24a.rlib" "/opt/rustwide/target/debug/deps/libeither-e56ae8568f7848ad.rlib" "/opt/rustwide/target/debug/deps/libcustom_derive-2cd77fb743b75f42.rlib" "/opt/rustwide/target/debug/deps/libcsv-de7d5cda0480bd1a.rlib" "/opt/rustwide/target/debug/deps/libryu-f59829dd55cb0771.rlib" "/opt/rustwide/target/debug/deps/libitoa-2e05c866ee66a047.rlib" "/opt/rustwide/target/debug/deps/libcsv_core-b2f0d5fa81297eae.rlib" "/opt/rustwide/target/debug/deps/libbstr-fba3200b735604ab.rlib" "/opt/rustwide/target/debug/deps/libregex_automata-046db2e2bbcd055f.rlib" "/opt/rustwide/target/debug/deps/libbyteorder-f7f925fcf7e16859.rlib" "/opt/rustwide/target/debug/deps/libbytecount-6c8e9209aefdc595.rlib" "/opt/rustwide/target/debug/deps/libbit_set-471554e6772bd36b.rlib" "/opt/rustwide/target/debug/deps/libbit_vec-a2e0abdfcd39fe2b.rlib" "/opt/rustwide/target/debug/deps/libapprox-06fb42c4ca8f5dba.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-63253226b9d79376.rlib" "/opt/rustwide/target/debug/deps/libbio_types-ab2ffa63cdd9b4ba.rlib" "/opt/rustwide/target/debug/deps/libserde-350a0862f57ed8cb.rlib" "/opt/rustwide/target/debug/deps/libregex-9d7cc8905e175b99.rlib" "/opt/rustwide/target/debug/deps/libthread_local-b5a8520d8d18b76f.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-a1e9e1e3fc23ae94.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-82571f279f177a2c.rlib" "/opt/rustwide/target/debug/deps/libmemchr-8df1994bb164e7a2.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-03dc560a77c5aa3e.rlib" "/opt/rustwide/target/debug/deps/libquick_error-e15ea4fce168f797.rlib" "-Wl,--start-group" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-d66e0ceb8eaec9b8.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-9717ec0599b569a0.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-04369de9ba916647.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-997d622c2e4dbe5c.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace-0359c4288a5ef89f.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace_sys-1b25ede22d698ab3.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-37940b486a68e488.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-06b77c27e794c7c6.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-4d07e02a8df36da1.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-fb29e0695c0a0f79.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-e16188b4cf97e8bb.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-5eb391c8dabdee77.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-b0689b528b222bee.rlib" "-Wl,--end-group" "/opt/rustwide/rustup-home/toolchains/beta-2020-07-24-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-ed072ac495e62e7a.rlib" "-Wl,-Bdynamic" "-llzma" "-lz" "-lutil" "-ldl" "-lutil" "-ldl" "-lrt" "-lpthread" "-lgcc_s" "-lc" "-lm" "-lrt" "-lpthread" "-lutil" "-ldl" "-lutil" [INFO] [stdout] = note: /usr/bin/ld: /opt/rustwide/target/debug/deps/librgsl-77eeeaa41aab4217.rlib(rgsl-77eeeaa41aab4217.rgsl.amjn3jem-cgu.11.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-77eeeaa41aab4217.rlib(rgsl-77eeeaa41aab4217.rgsl.amjn3jem-cgu.11.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-77eeeaa41aab4217.rlib(rgsl-77eeeaa41aab4217.rgsl.amjn3jem-cgu.9.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" "3d35ca507199d7d4628a813fe5ab92170b5fce693c8d155d7000e4ea96ebb737", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "3d35ca507199d7d4628a813fe5ab92170b5fce693c8d155d7000e4ea96ebb737", kill_on_drop: false }` [INFO] [stdout] 3d35ca507199d7d4628a813fe5ab92170b5fce693c8d155d7000e4ea96ebb737