[INFO] fetching crate libprosic 0.7.3... [INFO] testing libprosic-0.7.3 against 1.49.0 for beta-1.50-1 [INFO] extracting crate libprosic 0.7.3 into /workspace/builds/worker-13/source [INFO] validating manifest of crates.io crate libprosic 0.7.3 on toolchain 1.49.0 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.49.0" "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-13/source/Cargo.toml [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.49.0" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }` [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.49.0" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:b8eeb62f26c39b23691079a6cb6de528d8e88b4d71a8f6b1d30f8ba7d9c16de9" "/opt/rustwide/cargo-home/bin/cargo" "+1.49.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] f36fe50f27ab88c9727a5b172101111e1cb0fcb2cb704053802439bb3a26a25a [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" "f36fe50f27ab88c9727a5b172101111e1cb0fcb2cb704053802439bb3a26a25a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "f36fe50f27ab88c9727a5b172101111e1cb0fcb2cb704053802439bb3a26a25a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f36fe50f27ab88c9727a5b172101111e1cb0fcb2cb704053802439bb3a26a25a", kill_on_drop: false }` [INFO] [stdout] f36fe50f27ab88c9727a5b172101111e1cb0fcb2cb704053802439bb3a26a25a [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:b8eeb62f26c39b23691079a6cb6de528d8e88b4d71a8f6b1d30f8ba7d9c16de9" "/opt/rustwide/cargo-home/bin/cargo" "+1.49.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] a7bbb504172fe2261929edac3ac8b9566a7c2eb0c91115ff1d7c629bccd9f740 [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" "a7bbb504172fe2261929edac3ac8b9566a7c2eb0c91115ff1d7c629bccd9f740", kill_on_drop: false }` [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling itertools v0.6.5 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling ordered-float v1.1.1 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling ndarray v0.12.1 [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 num v0.1.42 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling bstr v0.2.14 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling csv v1.1.5 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling bio-types v0.7.0 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:62:20 [INFO] [stdout] | [INFO] [stdout] 62 | let variants = try!(utils::collect_variants( [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:70:21 [INFO] [stdout] | [INFO] [stdout] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:75:18 [INFO] [stdout] | [INFO] [stdout] 75 | Some(try!(joint_model.pileup( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:159:26 [INFO] [stdout] | [INFO] [stdout] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/model/sample.rs:76:17 [INFO] [stdout] | [INFO] [stdout] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 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 constant `std::sync::ONCE_INIT`: the `new` function is now preferred [INFO] [stdout] --> src/model/evidence/reads.rs:335:1 [INFO] [stdout] | [INFO] [stdout] 335 | / lazy_static! { [INFO] [stdout] 336 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stdout] 337 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in a macro (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `new` function is now preferred [INFO] [stdout] --> src/model/priors/single_cell_bulk.rs:26:1 [INFO] [stdout] | [INFO] [stdout] 26 | / cached! { [INFO] [stdout] 27 | | AMPLIF_CACHE: UnboundCache<(AlleleFreq, usize, usize), LogProb> = UnboundCache::new(); [INFO] [stdout] 28 | | // Lodato et al. 2015, Science, Supplementary Information, pages 8f and Fig. S5 (A, C, E) [INFO] [stdout] 29 | | // TODO: allow for non-default Lodato model parameters, e.g. learned from the data at hand [INFO] [stdout] ... | [INFO] [stdout] 96 | | } [INFO] [stdout] 97 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in a macro (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 33 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 39.00s [INFO] running `Command { std: "docker" "inspect" "a7bbb504172fe2261929edac3ac8b9566a7c2eb0c91115ff1d7c629bccd9f740", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a7bbb504172fe2261929edac3ac8b9566a7c2eb0c91115ff1d7c629bccd9f740", kill_on_drop: false }` [INFO] [stdout] a7bbb504172fe2261929edac3ac8b9566a7c2eb0c91115ff1d7c629bccd9f740 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-13/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "rustops/crates-build-env@sha256:b8eeb62f26c39b23691079a6cb6de528d8e88b4d71a8f6b1d30f8ba7d9c16de9" "/opt/rustwide/cargo-home/bin/cargo" "+1.49.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 89b3e7db03595cd2808ba67251f79bcdd10eda77ca6d687893e2b73ce835528c [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" "89b3e7db03595cd2808ba67251f79bcdd10eda77ca6d687893e2b73ce835528c", kill_on_drop: false }` [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling memchr v0.1.11 [INFO] [stderr] Compiling time v0.1.44 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] Compiling thread-id v2.0.0 [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:62:20 [INFO] [stdout] | [INFO] [stdout] 62 | let variants = try!(utils::collect_variants( [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:70:21 [INFO] [stdout] | [INFO] [stdout] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:75:18 [INFO] [stdout] | [INFO] [stdout] 75 | Some(try!(joint_model.pileup( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:159:26 [INFO] [stdout] | [INFO] [stdout] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/model/sample.rs:76:17 [INFO] [stdout] | [INFO] [stdout] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 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 constant `std::sync::ONCE_INIT`: the `new` function is now preferred [INFO] [stdout] --> src/model/evidence/reads.rs:335:1 [INFO] [stdout] | [INFO] [stdout] 335 | / lazy_static! { [INFO] [stdout] 336 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stdout] 337 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in a macro (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `new` function is now preferred [INFO] [stdout] --> src/model/priors/single_cell_bulk.rs:26:1 [INFO] [stdout] | [INFO] [stdout] 26 | / cached! { [INFO] [stdout] 27 | | AMPLIF_CACHE: UnboundCache<(AlleleFreq, usize, usize), LogProb> = UnboundCache::new(); [INFO] [stdout] 28 | | // Lodato et al. 2015, Science, Supplementary Information, pages 8f and Fig. S5 (A, C, E) [INFO] [stdout] 29 | | // TODO: allow for non-default Lodato model parameters, e.g. learned from the data at hand [INFO] [stdout] ... | [INFO] [stdout] 96 | | } [INFO] [stdout] 97 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in a macro (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 33 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling thread_local v0.2.7 [INFO] [stderr] Compiling aho-corasick v0.5.3 [INFO] [stderr] Compiling hyper v0.10.16 [INFO] [stderr] Compiling flate2 v0.2.20 [INFO] [stderr] Compiling regex v0.1.80 [INFO] [stderr] Compiling env_logger v0.3.5 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:62:20 [INFO] [stdout] | [INFO] [stdout] 62 | let variants = try!(utils::collect_variants( [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:70:21 [INFO] [stdout] | [INFO] [stdout] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:75:18 [INFO] [stdout] | [INFO] [stdout] 75 | Some(try!(joint_model.pileup( [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/call/pairwise.rs:159:26 [INFO] [stdout] | [INFO] [stdout] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated macro `try`: use the `?` operator instead [INFO] [stdout] --> src/model/sample.rs:76:17 [INFO] [stdout] | [INFO] [stdout] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 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 constant `std::sync::ONCE_INIT`: the `new` function is now preferred [INFO] [stdout] --> src/model/evidence/reads.rs:335:1 [INFO] [stdout] | [INFO] [stdout] 335 | / lazy_static! { [INFO] [stdout] 336 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stdout] 337 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in a macro (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated constant `std::sync::ONCE_INIT`: the `new` function is now preferred [INFO] [stdout] --> src/model/priors/single_cell_bulk.rs:26:1 [INFO] [stdout] | [INFO] [stdout] 26 | / cached! { [INFO] [stdout] 27 | | AMPLIF_CACHE: UnboundCache<(AlleleFreq, usize, usize), LogProb> = UnboundCache::new(); [INFO] [stdout] 28 | | // Lodato et al. 2015, Science, Supplementary Information, pages 8f and Fig. S5 (A, C, E) [INFO] [stdout] 29 | | // TODO: allow for non-default Lodato model parameters, e.g. learned from the data at hand [INFO] [stdout] ... | [INFO] [stdout] 96 | | } [INFO] [stdout] 97 | | } [INFO] [stdout] | |_^ [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in a macro (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: this method call currently resolves to `<&[T; N] as IntoIterator>::into_iter` (due to autoref coercions), but that might change in the future when `IntoIterator` impls for arrays are added. [INFO] [stdout] --> src/model/sample.rs:612:79 [INFO] [stdout] | [INFO] [stdout] 612 | for (record, true_alt_prob) in records.into_iter().zip(true_alt_probs.into_iter()) { [INFO] [stdout] | ^^^^^^^^^ help: use `.iter()` instead of `.into_iter()` to avoid ambiguity: `iter` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(array_into_iter)]` on by default [INFO] [stdout] = warning: this was previously accepted by the compiler but is being phased out; it will become a hard error in a future release! [INFO] [stdout] = note: for more information, see issue #66145 [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: linking with `cc` failed: exit code: 1 [INFO] [stdout] | [INFO] [stdout] = note: "cc" "-Wl,--as-needed" "-Wl,-z,noexecstack" "-m64" "-Wl,--eh-frame-hdr" "-L" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.0.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.1.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.10.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.11.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.12.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.13.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.14.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.15.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.2.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.3.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.4.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.5.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.6.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.7.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.8.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.libprosic.em17yaj0-cgu.9.rcgu.o" "-o" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000" "/opt/rustwide/target/debug/deps/libprosic-c8490c834fd63000.1buhygtb8g355rqv.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-f439fb67761f81e0/out" "-L" "/opt/rustwide/target/debug/build/rust-htslib-54381ee693944c30/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-a45e95dcb3abc346/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libtest-6609e81d71a1bf05.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libterm-c352aab3e89370e6.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgetopts-5a89b15f567bd092.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunicode_width-f48d3ad387757b0f.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_std-bf2dc5d6d88f70a5.rlib" "/opt/rustwide/target/debug/deps/libenv_logger-ba4e7080a225eec5.rlib" "/opt/rustwide/target/debug/deps/libregex-04a44951f3ebb99f.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-fb8365ae1d572763.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-0c1978a6494a135e.rlib" "/opt/rustwide/target/debug/deps/libthread_local-451c388915bf7bad.rlib" "/opt/rustwide/target/debug/deps/libthread_id-6356a7f5ace5ab7c.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-511e736ca47c71a1.rlib" "/opt/rustwide/target/debug/deps/libmemchr-312f01f15b66e9da.rlib" "/opt/rustwide/target/debug/deps/libcached-264da91799126a30.rlib" "/opt/rustwide/target/debug/deps/libregex-febeba390744a425.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-1eb514de9d1ddb83.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-68f5994dbf13cd18.rlib" "/opt/rustwide/target/debug/deps/libucd_util-616fa98346e14cde.rlib" "/opt/rustwide/target/debug/deps/libthread_local-b6fc34b76e7c6508.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-38160ad4e0bc9c96.rlib" "/opt/rustwide/target/debug/deps/librusty_machine-328da9fb004d2686.rlib" "/opt/rustwide/target/debug/deps/librulinalg-6a5660509e719f2b.rlib" "/opt/rustwide/target/debug/deps/libnum-81b49377de24033f.rlib" "/opt/rustwide/target/debug/deps/libnum_iter-63eb6f71941d397c.rlib" "/opt/rustwide/target/debug/deps/libndarray-e41cffb9dbeb179c.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-50084b4fa9deb616.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-890f5353c77588cc.rlib" "/opt/rustwide/target/debug/deps/libitertools-2733fbcf6be9c4d5.rlib" "/opt/rustwide/target/debug/deps/libapprox-a8e85ad9a60368e3.rlib" "/opt/rustwide/target/debug/deps/librgsl-7acaba4e3684f76e.rlib" "/opt/rustwide/target/debug/deps/libc_vec-1dfec5b3fb2e2197.rlib" "/opt/rustwide/target/debug/deps/liblog-2ccdee9e6280c915.rlib" "/opt/rustwide/target/debug/deps/liblog-e85f58044ae91ffe.rlib" "/opt/rustwide/target/debug/deps/libcfg_if-b10e0993eefc366b.rlib" "/opt/rustwide/target/debug/deps/librust_htslib-97eda4d2c325d294.rlib" "/opt/rustwide/target/debug/deps/liblzma_sys-a22d316a6d7809fa.rlib" "/opt/rustwide/target/debug/deps/libbzip2_sys-f6117c9e1e283246.rlib" "/opt/rustwide/target/debug/deps/liblibz_sys-418d21753b80c667.rlib" "/opt/rustwide/target/debug/deps/liblinear_map-48ab514202f9e8ab.rlib" "/opt/rustwide/target/debug/deps/liburl-b1ad55a490a79752.rlib" "/opt/rustwide/target/debug/deps/libpercent_encoding-6cfaa5fc89ff72d4.rlib" "/opt/rustwide/target/debug/deps/libidna-740fe4d95ebee3ae.rlib" "/opt/rustwide/target/debug/deps/libunicode_normalization-00a5caef43a4386b.rlib" "/opt/rustwide/target/debug/deps/libtinyvec-c7495963f757b92a.rlib" "/opt/rustwide/target/debug/deps/libtinyvec_macros-5b1520f36949599c.rlib" "/opt/rustwide/target/debug/deps/libunicode_bidi-7e8075a07f0e5422.rlib" "/opt/rustwide/target/debug/deps/libmatches-5499bb0a916b29b9.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-9850e1ed257f46c2.rlib" "/opt/rustwide/target/debug/deps/libitertools-bfde21da67186f50.rlib" "/opt/rustwide/target/debug/deps/libieee754-425be751f74d7b53.rlib" "/opt/rustwide/target/debug/deps/libbitflags-2b6fb6d6fa47ec16.rlib" "/opt/rustwide/target/debug/deps/libbio-c9f1e7951e2cc1fd.rlib" "/opt/rustwide/target/debug/deps/libfxhash-f65c3b33174b94ed.rlib" "/opt/rustwide/target/debug/deps/libvec_map-7ca69cbc23ef8187.rlib" "/opt/rustwide/target/debug/deps/libstatrs-49e95b0192ab3cce.rlib" "/opt/rustwide/target/debug/deps/librand-20ebdf843e0d1e8a.rlib" "/opt/rustwide/target/debug/deps/librand-dbec611a3fbfbe17.rlib" "/opt/rustwide/target/debug/deps/liblibc-a8fd1e8bab0f1b54.rlib" "/opt/rustwide/target/debug/deps/libfnv-751e5967119454f8.rlib" "/opt/rustwide/target/debug/deps/libbv-1150c6eb49bd5190.rlib" "/opt/rustwide/target/debug/deps/libordered_float-f4781aabfb2f2bf5.rlib" "/opt/rustwide/target/debug/deps/libnum_integer-4545f17f749a0151.rlib" "/opt/rustwide/target/debug/deps/libnewtype_derive-ffe04384b7e78789.rlib" "/opt/rustwide/target/debug/deps/libndarray-e78756ee144e5be6.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-9d375b9bf1e454af.rlib" "/opt/rustwide/target/debug/deps/libmatrixmultiply-ccebb5c2cb4b358a.rlib" "/opt/rustwide/target/debug/deps/librawpointer-647b381188995d1f.rlib" "/opt/rustwide/target/debug/deps/libmultimap-32d9a72007a058fb.rlib" "/opt/rustwide/target/debug/deps/libitertools_num-b91c96631b6205e5.rlib" "/opt/rustwide/target/debug/deps/libitertools-f8736e4bd63a17f7.rlib" "/opt/rustwide/target/debug/deps/libeither-6531171134b8f25b.rlib" "/opt/rustwide/target/debug/deps/libcustom_derive-4dd08374a6d148b5.rlib" "/opt/rustwide/target/debug/deps/libcsv-db6c65727a644233.rlib" "/opt/rustwide/target/debug/deps/libryu-37b6e9a22bb2209d.rlib" "/opt/rustwide/target/debug/deps/libitoa-6048d71bcce27ffd.rlib" "/opt/rustwide/target/debug/deps/libcsv_core-57f923abb6b113c2.rlib" "/opt/rustwide/target/debug/deps/libbstr-b0c137b0bd6718aa.rlib" "/opt/rustwide/target/debug/deps/libregex_automata-bce0cc856190d472.rlib" "/opt/rustwide/target/debug/deps/libbyteorder-04b16b37fbc1beb3.rlib" "/opt/rustwide/target/debug/deps/libbytecount-6660cb18f7414cb5.rlib" "/opt/rustwide/target/debug/deps/libbit_set-a0c1b6bd36be8ca8.rlib" "/opt/rustwide/target/debug/deps/libbit_vec-606d5bed1aa32ae2.rlib" "/opt/rustwide/target/debug/deps/libapprox-ec5b8b9b690696f9.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-4a59219676fe7595.rlib" "/opt/rustwide/target/debug/deps/libbio_types-4857b8d7057ec4eb.rlib" "/opt/rustwide/target/debug/deps/libserde-0f682e824bd4c674.rlib" "/opt/rustwide/target/debug/deps/libregex-62e055e6c3a1f4aa.rlib" "/opt/rustwide/target/debug/deps/libthread_local-76e36b18ae5ab5a5.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-2b91d401512672d8.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-e01381020880b078.rlib" "/opt/rustwide/target/debug/deps/libmemchr-e03602aba27a22bc.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-7895c92c6d278491.rlib" "/opt/rustwide/target/debug/deps/libquick_error-02525b70077f996f.rlib" "-Wl,--start-group" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-e12de7683a34c500.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-446a53c2e468675f.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libminiz_oxide-86fef9fb252a2d33.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libadler-3bed9bfd30304751.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libobject-0e38eeb474a7b386.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libaddr2line-a846ed547b824740.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgimli-c9540f0a4fb9265d.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-7d2ca66c92c356eb.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-147e2c808f949493.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-bd2a4369506670e9.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-74bfdd0ce7d0ed48.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-6777f47f1c491841.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-b104f1790174f2be.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-db37898996f45c13.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-25b7435131fc4938.rlib" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-9d4b6f3c097e876e.rlib" "-Wl,--end-group" "/opt/rustwide/rustup-home/toolchains/1.49.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-3f953ad652ab829a.rlib" "-Wl,-Bdynamic" "-llzma" "-lz" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" [INFO] [stdout] = note: /usr/bin/ld: /opt/rustwide/target/debug/deps/librgsl-7acaba4e3684f76e.rlib(rgsl-7acaba4e3684f76e.rgsl.3lfht79f-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-7acaba4e3684f76e.rlib(rgsl-7acaba4e3684f76e.rgsl.3lfht79f-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-7acaba4e3684f76e.rlib(rgsl-7acaba4e3684f76e.rgsl.3lfht79f-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" "89b3e7db03595cd2808ba67251f79bcdd10eda77ca6d687893e2b73ce835528c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "89b3e7db03595cd2808ba67251f79bcdd10eda77ca6d687893e2b73ce835528c", kill_on_drop: false }` [INFO] [stdout] 89b3e7db03595cd2808ba67251f79bcdd10eda77ca6d687893e2b73ce835528c