[INFO] crate libprosic 0.7.3 is already in cache [INFO] testing libprosic-0.7.3 against 1.45.2 for beta-1.46-1 [INFO] extracting crate libprosic 0.7.3 into /workspace/builds/worker-14/source [INFO] validating manifest of crates.io crate libprosic 0.7.3 on toolchain 1.45.2 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.45.2" "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-14/source/Cargo.toml [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.45.2" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.45.2" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/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" "+1.45.2" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] e7f606c0dc854ff348a535b31cb476ee5e3f4a6e6c0ee706ea082c3e15fe7936 [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" "e7f606c0dc854ff348a535b31cb476ee5e3f4a6e6c0ee706ea082c3e15fe7936", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "e7f606c0dc854ff348a535b31cb476ee5e3f4a6e6c0ee706ea082c3e15fe7936", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e7f606c0dc854ff348a535b31cb476ee5e3f4a6e6c0ee706ea082c3e15fe7936", kill_on_drop: false }` [INFO] [stdout] e7f606c0dc854ff348a535b31cb476ee5e3f4a6e6c0ee706ea082c3e15fe7936 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/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" "+1.45.2" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 1eb9dc87457e71f7a7c63e6201622b73cec7a624f6270b93921e4d6f536c6240 [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" "1eb9dc87457e71f7a7c63e6201622b73cec7a624f6270b93921e4d6f536c6240", kill_on_drop: false }` [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling linear-map v1.2.0 [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 num-integer v0.1.43 [INFO] [stderr] Compiling num-iter v0.1.41 [INFO] [stderr] Compiling lzma-sys v0.1.16 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling aho-corasick v0.6.10 [INFO] [stderr] Compiling csv-core v0.1.10 [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 approx v0.3.2 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling bstr v0.2.13 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling clap v2.33.2 [INFO] [stderr] Compiling num v0.1.42 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling csv v1.1.3 [INFO] [stderr] Compiling bio-types v0.7.0 [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 58.55s [INFO] running `Command { std: "docker" "inspect" "1eb9dc87457e71f7a7c63e6201622b73cec7a624f6270b93921e4d6f536c6240", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1eb9dc87457e71f7a7c63e6201622b73cec7a624f6270b93921e4d6f536c6240", kill_on_drop: false }` [INFO] [stdout] 1eb9dc87457e71f7a7c63e6201622b73cec7a624f6270b93921e4d6f536c6240 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/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" "+1.45.2" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] ba6cd8d238ee896875e0cd234d523d3eb39f46feb17144d5ab6bad4a5c1868d6 [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" "ba6cd8d238ee896875e0cd234d523d3eb39f46feb17144d5ab6bad4a5c1868d6", kill_on_drop: false }` [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] Compiling hyper v0.10.16 [INFO] [stderr] Compiling regex v0.1.80 [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 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! 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"/opt/rustwide/target/debug/deps/libprosic-57fb0542b265873c.3z2jzg3uogz8j08h.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-93892b05cb76ce5f/out" "-L" "/opt/rustwide/target/debug/build/rust-htslib-c1bf999b4bab5ef0/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-05dfc8dd7581782a/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libtest-3ad1ab5f7ba3783f.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libterm-be4838eb8e86accd.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgetopts-d7f97d30aca9ddf1.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunicode_width-2e806a0559ee0b3f.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_std-9137a404219e7a82.rlib" "/opt/rustwide/target/debug/deps/libenv_logger-789d793dc7c6c039.rlib" "/opt/rustwide/target/debug/deps/libregex-d14b20db89782b0d.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-1b3b285a776af71f.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-58f920edbab8102e.rlib" "/opt/rustwide/target/debug/deps/libthread_local-5d96dd696e4b31dd.rlib" "/opt/rustwide/target/debug/deps/libthread_id-204fca3d33a7054c.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-382101a57e51e913.rlib" "/opt/rustwide/target/debug/deps/libmemchr-8b2c571c5974d1f9.rlib" "/opt/rustwide/target/debug/deps/libcached-ba1dc178846c616f.rlib" "/opt/rustwide/target/debug/deps/libregex-a04e4df337595851.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-0c6a5d69c0e61c67.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-73b9402cc491e1f8.rlib" "/opt/rustwide/target/debug/deps/libucd_util-cf5f24969cc5fdd5.rlib" "/opt/rustwide/target/debug/deps/libthread_local-57d16560e5d8559d.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-b06f85a5a3557e51.rlib" "/opt/rustwide/target/debug/deps/librusty_machine-d40ed8de54854161.rlib" "/opt/rustwide/target/debug/deps/librulinalg-636c95ca524b231e.rlib" "/opt/rustwide/target/debug/deps/libnum-e3679838df648afd.rlib" "/opt/rustwide/target/debug/deps/libnum_iter-f733c6b77dc722ee.rlib" "/opt/rustwide/target/debug/deps/libndarray-b4a8977cf1def9d0.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-d20be82f95619b5e.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-6615e9d03ffe16c6.rlib" "/opt/rustwide/target/debug/deps/libitertools-2fd721d8215b5ca6.rlib" "/opt/rustwide/target/debug/deps/libapprox-f318ba0767cda520.rlib" "/opt/rustwide/target/debug/deps/librgsl-a8753f01c38e0927.rlib" "/opt/rustwide/target/debug/deps/libc_vec-69221a5c5d036258.rlib" "/opt/rustwide/target/debug/deps/liblog-8d6deb05e4a450a5.rlib" "/opt/rustwide/target/debug/deps/liblog-f4faf1fa578e34f7.rlib" "/opt/rustwide/target/debug/deps/libcfg_if-ab1bd98be96b57b3.rlib" "/opt/rustwide/target/debug/deps/librust_htslib-127c3346301bc830.rlib" "/opt/rustwide/target/debug/deps/liblzma_sys-c13adee91deba707.rlib" "/opt/rustwide/target/debug/deps/libbzip2_sys-9bf9d2b774066a5d.rlib" "/opt/rustwide/target/debug/deps/liblibz_sys-bdeca5ba0e829c3b.rlib" "/opt/rustwide/target/debug/deps/liblinear_map-a79294a4bbb33dc4.rlib" "/opt/rustwide/target/debug/deps/liburl-33bbacdddff76213.rlib" "/opt/rustwide/target/debug/deps/libpercent_encoding-a4b5f53972b66b35.rlib" "/opt/rustwide/target/debug/deps/libidna-b8d4ad66d49965ce.rlib" "/opt/rustwide/target/debug/deps/libunicode_normalization-32d152a46851e25f.rlib" "/opt/rustwide/target/debug/deps/libtinyvec-6b37295460e5f9d5.rlib" "/opt/rustwide/target/debug/deps/libunicode_bidi-a35d543dc62ca9dc.rlib" "/opt/rustwide/target/debug/deps/libmatches-2e3ca713d4d6e5d2.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-cbf4e74d25b393ff.rlib" "/opt/rustwide/target/debug/deps/libitertools-c4fbde7601dfe63b.rlib" "/opt/rustwide/target/debug/deps/libieee754-94bae874445bfd89.rlib" "/opt/rustwide/target/debug/deps/libbitflags-7de30104f198441d.rlib" "/opt/rustwide/target/debug/deps/libbio-150c4dc8d7747fd3.rlib" "/opt/rustwide/target/debug/deps/libfxhash-a8507059d45d10e0.rlib" "/opt/rustwide/target/debug/deps/libvec_map-648300f33b5f6c66.rlib" "/opt/rustwide/target/debug/deps/libstatrs-79c4d98733492c78.rlib" "/opt/rustwide/target/debug/deps/librand-6669495e55f7c028.rlib" "/opt/rustwide/target/debug/deps/librand-de20e51950031d36.rlib" "/opt/rustwide/target/debug/deps/liblibc-45fdab7f729c9106.rlib" "/opt/rustwide/target/debug/deps/libfnv-5a2e7315855d9083.rlib" "/opt/rustwide/target/debug/deps/libbv-c0135f2efdba0e6b.rlib" "/opt/rustwide/target/debug/deps/libordered_float-6cc00a2c13773728.rlib" "/opt/rustwide/target/debug/deps/libnum_integer-f84db87ac40dfc9a.rlib" "/opt/rustwide/target/debug/deps/libnewtype_derive-93d9b6e473048c88.rlib" "/opt/rustwide/target/debug/deps/libndarray-68808e7bdebf0c81.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-c2a60ba613427157.rlib" "/opt/rustwide/target/debug/deps/libmatrixmultiply-a24ba743202aeda9.rlib" "/opt/rustwide/target/debug/deps/librawpointer-e0d1c574149d8417.rlib" "/opt/rustwide/target/debug/deps/libmultimap-e5c24ed61f0580b2.rlib" "/opt/rustwide/target/debug/deps/libitertools_num-8160778a766926b7.rlib" "/opt/rustwide/target/debug/deps/libitertools-b382d5ccb481bb7a.rlib" "/opt/rustwide/target/debug/deps/libeither-73ae1ee3c5bcec7c.rlib" "/opt/rustwide/target/debug/deps/libcustom_derive-f2782116694d7236.rlib" "/opt/rustwide/target/debug/deps/libcsv-5be82b0b29c568c8.rlib" "/opt/rustwide/target/debug/deps/libryu-346252d1dd2293b6.rlib" "/opt/rustwide/target/debug/deps/libitoa-571136415771b7fa.rlib" "/opt/rustwide/target/debug/deps/libcsv_core-ddbfc52e68a90bfc.rlib" "/opt/rustwide/target/debug/deps/libbstr-5b224445bb3d06c5.rlib" "/opt/rustwide/target/debug/deps/libregex_automata-496d99fa54fdb2a1.rlib" "/opt/rustwide/target/debug/deps/libbyteorder-8b927a909cceb876.rlib" "/opt/rustwide/target/debug/deps/libbytecount-effa57ff73b6dee8.rlib" "/opt/rustwide/target/debug/deps/libbit_set-7977f767fc520d57.rlib" "/opt/rustwide/target/debug/deps/libbit_vec-c168fedb2041c9fb.rlib" "/opt/rustwide/target/debug/deps/libapprox-9ea2d41b6f97e919.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-dab92e4a7c3b6ca2.rlib" "/opt/rustwide/target/debug/deps/libbio_types-c85bb8ddf4cc10fd.rlib" "/opt/rustwide/target/debug/deps/libserde-598de5243122c81b.rlib" "/opt/rustwide/target/debug/deps/libregex-347800da6df6c271.rlib" "/opt/rustwide/target/debug/deps/libthread_local-87cfd577652377a1.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-c234f626249548c1.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-97b2f11ab4a5d4c6.rlib" "/opt/rustwide/target/debug/deps/libmemchr-994f1cb85517744c.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-660ab907323d6aba.rlib" "/opt/rustwide/target/debug/deps/libquick_error-c22e30eaeceace11.rlib" "-Wl,--start-group" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-8bb11f807a7b6b4c.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-ca8087507780d964.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-259c92b387c1c166.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-16e0a2fbbb8e14b3.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace-8a1651b8e23d2aaf.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace_sys-23bdd98b0574083e.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-855a92055ec33e2e.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-24c70dd44fbacdfb.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-b326273841bae587.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-ac3c1f0e16507051.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-a5729542b65954aa.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-09bd1119ab1cad7d.rlib" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-9a787681bfbeaf61.rlib" "-Wl,--end-group" "/opt/rustwide/rustup-home/toolchains/1.45.2-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-5a0398ee67f74664.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-a8753f01c38e0927.rlib(rgsl-a8753f01c38e0927.rgsl.qes6giqo-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-a8753f01c38e0927.rlib(rgsl-a8753f01c38e0927.rgsl.qes6giqo-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-a8753f01c38e0927.rlib(rgsl-a8753f01c38e0927.rgsl.qes6giqo-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" "ba6cd8d238ee896875e0cd234d523d3eb39f46feb17144d5ab6bad4a5c1868d6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ba6cd8d238ee896875e0cd234d523d3eb39f46feb17144d5ab6bad4a5c1868d6", kill_on_drop: false }` [INFO] [stdout] ba6cd8d238ee896875e0cd234d523d3eb39f46feb17144d5ab6bad4a5c1868d6