[INFO] crate libprosic 0.7.3 is already in cache [INFO] testing libprosic-0.7.3 against 1.38.0 for beta-1.39-1 [INFO] extracting crate libprosic 0.7.3 into work/builds/worker-0/source [INFO] validating manifest of crates.io crate libprosic 0.7.3 on toolchain 1.38.0 [INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+1.38.0" "read-manifest" "--manifest-path" "Cargo.toml"` [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 work/builds/worker-0/source/Cargo.toml [INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+1.38.0" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+1.38.0" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-0/source:/opt/rustwide/workdir:ro,Z" "-v" "/big/crater/work/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/big/crater/work/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=1000" "-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" "/opt/rustwide/cargo-home/bin/cargo" "+1.38.0" "build" "--frozen"` [INFO] [stdout] 54da1c433893bc929ed8d01ab6008c676db898405775dcc94f0f1384d316c62c [INFO] running `"docker" "start" "-a" "54da1c433893bc929ed8d01ab6008c676db898405775dcc94f0f1384d316c62c"` [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling rawpointer v0.1.0 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling c_vec v1.0.12 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling num-complex v0.2.3 [INFO] [stderr] Compiling bzip2-sys v0.1.7 [INFO] [stderr] Compiling lzma-sys v0.1.15 [INFO] [stderr] Compiling fs-utils v1.1.1 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling itertools v0.6.5 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling memchr v2.2.1 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling num v0.1.42 [INFO] [stderr] Compiling vec_map v0.8.1 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling aho-corasick v0.7.6 [INFO] [stderr] Compiling aho-corasick v0.6.10 [INFO] [stderr] Compiling csv-core v0.1.6 [INFO] [stderr] Compiling bstr v0.2.8 [INFO] [stderr] Compiling clap v2.33.0 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling csv v1.1.1 [INFO] [stderr] Compiling regex v1.3.1 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling bio-types v0.5.1 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call/pairwise.rs:55:62 [INFO] [stderr] | [INFO] [stderr] 55 | ) -> Result>>, Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(bare_trait_objects)]` on by default [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call/pairwise.rs:116:21 [INFO] [stderr] | [INFO] [stderr] 116 | ) -> Result<(), Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/alignment_properties.rs:40:68 [INFO] [stderr] | [INFO] [stderr] 40 | pub fn estimate(bam: &mut R) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/alignment_properties.rs:142:33 [INFO] [stderr] | [INFO] [stderr] 142 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/fdr/ev.rs:35:21 [INFO] [stderr] | [INFO] [stderr] 35 | ) -> Result<(), Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:52:89 [INFO] [stderr] | [INFO] [stderr] 52 | pub fn estimate_insert_size(left: &bam::Record, right: &bam::Record) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:56:68 [INFO] [stderr] | [INFO] [stderr] 56 | let aln = |rec: &bam::Record, cigar| -> Result<(u32, u32), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:120:41 [INFO] [stderr] | [INFO] [stderr] 120 | ) -> Result<(LogProb, LogProb), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:30:49 [INFO] [stderr] | [INFO] [stderr] 30 | ) -> Result, Box>; [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:56:49 [INFO] [stderr] | [INFO] [stderr] 56 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:101:49 [INFO] [stderr] | [INFO] [stderr] 101 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:169:49 [INFO] [stderr] | [INFO] [stderr] 169 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:68:82 [INFO] [stderr] | [INFO] [stderr] 68 | pub fn fill(&mut self, chrom: &[u8], start: u32, end: u32) -> Result<(), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:220:39 [INFO] [stderr] | [INFO] [stderr] 220 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:362:42 [INFO] [stderr] | [INFO] [stderr] 362 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:363:34 [INFO] [stderr] | [INFO] [stderr] 363 | let mut evidence: RefMut = match variant { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn evidence::reads::AbstractReadEvidence` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:409:42 [INFO] [stderr] | [INFO] [stderr] 409 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:412:44 [INFO] [stderr] | [INFO] [stderr] 412 | -> Result<(LogProb, LogProb), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/mod.rs:275:41 [INFO] [stderr] | [INFO] [stderr] 275 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/mod.rs:416:42 [INFO] [stderr] | [INFO] [stderr] 416 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:27:46 [INFO] [stderr] | [INFO] [stderr] 27 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:204:62 [INFO] [stderr] | [INFO] [stderr] 204 | pub fn seq(&mut self, chrom: &[u8]) -> Result<&[u8], Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:232:39 [INFO] [stderr] | [INFO] [stderr] 232 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:276:35 [INFO] [stderr] | [INFO] [stderr] 276 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:317:21 [INFO] [stderr] | [INFO] [stderr] 317 | ) -> Result<(), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:367:30 [INFO] [stderr] | [INFO] [stderr] 367 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'std::sync::ONCE_INIT': the `new` function is now preferred [INFO] [stderr] --> src/model/evidence/reads.rs:335:1 [INFO] [stderr] | [INFO] [stderr] 335 | / lazy_static! { [INFO] [stderr] 336 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stderr] 337 | | } [INFO] [stderr] | |_^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(deprecated)]` on by default [INFO] [stderr] = note: this warning originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'std::sync::ONCE_INIT': the `new` function is now preferred [INFO] [stderr] --> src/model/priors/single_cell_bulk.rs:26:1 [INFO] [stderr] | [INFO] [stderr] 26 | / cached! { [INFO] [stderr] 27 | | AMPLIF_CACHE: UnboundCache<(AlleleFreq, usize, usize), LogProb> = UnboundCache::new(); [INFO] [stderr] 28 | | // Lodato et al. 2015, Science, Supplementary Information, pages 8f and Fig. S5 (A, C, E) [INFO] [stderr] 29 | | // TODO: allow for non-default Lodato model parameters, e.g. learned from the data at hand [INFO] [stderr] ... | [INFO] [stderr] 96 | | } [INFO] [stderr] 97 | | } [INFO] [stderr] | |_^ [INFO] [stderr] | [INFO] [stderr] = note: this warning originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 40.29s [INFO] running `"docker" "inspect" "54da1c433893bc929ed8d01ab6008c676db898405775dcc94f0f1384d316c62c"` [INFO] running `"docker" "rm" "-f" "54da1c433893bc929ed8d01ab6008c676db898405775dcc94f0f1384d316c62c"` [INFO] [stdout] 54da1c433893bc929ed8d01ab6008c676db898405775dcc94f0f1384d316c62c [INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-0/source:/opt/rustwide/workdir:ro,Z" "-v" "/big/crater/work/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/big/crater/work/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=1000" "-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" "/opt/rustwide/cargo-home/bin/cargo" "+1.38.0" "test" "--frozen" "--no-run"` [INFO] [stdout] d8ac7ee729ff731e82b05836f0e18900a40d4d57ef08f0d7200c68398c6a67e1 [INFO] running `"docker" "start" "-a" "d8ac7ee729ff731e82b05836f0e18900a40d4d57ef08f0d7200c68398c6a67e1"` [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling memchr v0.1.11 [INFO] [stderr] Compiling thread-id v2.0.0 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] Compiling hyper v0.10.16 [INFO] [stderr] Compiling thread_local v0.2.7 [INFO] [stderr] Compiling aho-corasick v0.5.3 [INFO] [stderr] Compiling regex v0.1.80 [INFO] [stderr] Compiling flate2 v0.2.20 [INFO] [stderr] Compiling env_logger v0.3.5 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call/pairwise.rs:55:62 [INFO] [stderr] | [INFO] [stderr] 55 | ) -> Result>>, Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(bare_trait_objects)]` on by default [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call/pairwise.rs:116:21 [INFO] [stderr] | [INFO] [stderr] 116 | ) -> Result<(), Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/alignment_properties.rs:40:68 [INFO] [stderr] | [INFO] [stderr] 40 | pub fn estimate(bam: &mut R) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/alignment_properties.rs:142:33 [INFO] [stderr] | [INFO] [stderr] 142 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/fdr/ev.rs:35:21 [INFO] [stderr] | [INFO] [stderr] 35 | ) -> Result<(), Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:52:89 [INFO] [stderr] | [INFO] [stderr] 52 | pub fn estimate_insert_size(left: &bam::Record, right: &bam::Record) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:56:68 [INFO] [stderr] | [INFO] [stderr] 56 | let aln = |rec: &bam::Record, cigar| -> Result<(u32, u32), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:120:41 [INFO] [stderr] | [INFO] [stderr] 120 | ) -> Result<(LogProb, LogProb), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:30:49 [INFO] [stderr] | [INFO] [stderr] 30 | ) -> Result, Box>; [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:56:49 [INFO] [stderr] | [INFO] [stderr] 56 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:101:49 [INFO] [stderr] | [INFO] [stderr] 101 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:169:49 [INFO] [stderr] | [INFO] [stderr] 169 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:68:82 [INFO] [stderr] | [INFO] [stderr] 68 | pub fn fill(&mut self, chrom: &[u8], start: u32, end: u32) -> Result<(), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:220:39 [INFO] [stderr] | [INFO] [stderr] 220 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:362:42 [INFO] [stderr] | [INFO] [stderr] 362 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:363:34 [INFO] [stderr] | [INFO] [stderr] 363 | let mut evidence: RefMut = match variant { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn evidence::reads::AbstractReadEvidence` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:409:42 [INFO] [stderr] | [INFO] [stderr] 409 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:412:44 [INFO] [stderr] | [INFO] [stderr] 412 | -> Result<(LogProb, LogProb), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/mod.rs:275:41 [INFO] [stderr] | [INFO] [stderr] 275 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/mod.rs:416:42 [INFO] [stderr] | [INFO] [stderr] 416 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:27:46 [INFO] [stderr] | [INFO] [stderr] 27 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:204:62 [INFO] [stderr] | [INFO] [stderr] 204 | pub fn seq(&mut self, chrom: &[u8]) -> Result<&[u8], Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:232:39 [INFO] [stderr] | [INFO] [stderr] 232 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:276:35 [INFO] [stderr] | [INFO] [stderr] 276 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:317:21 [INFO] [stderr] | [INFO] [stderr] 317 | ) -> Result<(), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:367:30 [INFO] [stderr] | [INFO] [stderr] 367 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'std::sync::ONCE_INIT': the `new` function is now preferred [INFO] [stderr] --> src/model/evidence/reads.rs:335:1 [INFO] [stderr] | [INFO] [stderr] 335 | / lazy_static! { [INFO] [stderr] 336 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stderr] 337 | | } [INFO] [stderr] | |_^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(deprecated)]` on by default [INFO] [stderr] = note: this warning originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'std::sync::ONCE_INIT': the `new` function is now preferred [INFO] [stderr] --> src/model/priors/single_cell_bulk.rs:26:1 [INFO] [stderr] | [INFO] [stderr] 26 | / cached! { [INFO] [stderr] 27 | | AMPLIF_CACHE: UnboundCache<(AlleleFreq, usize, usize), LogProb> = UnboundCache::new(); [INFO] [stderr] 28 | | // Lodato et al. 2015, Science, Supplementary Information, pages 8f and Fig. S5 (A, C, E) [INFO] [stderr] 29 | | // TODO: allow for non-default Lodato model parameters, e.g. learned from the data at hand [INFO] [stderr] ... | [INFO] [stderr] 96 | | } [INFO] [stderr] 97 | | } [INFO] [stderr] | |_^ [INFO] [stderr] | [INFO] [stderr] = note: this warning originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] error: linking with `cc` failed: exit code: 1 [INFO] [stderr] | [INFO] [stderr] = note: "cc" "-Wl,--as-needed" "-Wl,-z,noexecstack" "-m64" "-L" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.0.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.1.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.10.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.11.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.12.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.13.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.14.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.15.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.2.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.3.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.4.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.5.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.6.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.7.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.8.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.libprosic.d718cizn-cgu.9.rcgu.o" "-o" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd" "/opt/rustwide/target/debug/deps/libprosic-e8122ec2e1f77efd.3ndoivm4zam9d27g.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-bf8c3bace5d1d440/out" "-L" "/opt/rustwide/target/debug/build/rust-htslib-8c21a271fb00d2ec/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-2525a4b265074c33/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libtest-8b6fbd25e1766083.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libterm-bd8f21e3bdd6cbdc.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgetopts-bfcad117c6a632af.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunicode_width-79a1f91e8ce4eb83.rlib" "/opt/rustwide/target/debug/deps/libenv_logger-a8c4d6d5ab69d463.rlib" "/opt/rustwide/target/debug/deps/libregex-e5747411d3334cab.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-be9b532c7b2a32f6.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-c182adb4258878f6.rlib" "/opt/rustwide/target/debug/deps/libthread_local-e47bbb879e5c1645.rlib" "/opt/rustwide/target/debug/deps/libthread_id-94a04b7d533b69b1.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-89048c40b7043939.rlib" "/opt/rustwide/target/debug/deps/libmemchr-e679e3bf313dbfa7.rlib" "/opt/rustwide/target/debug/deps/libcached-2f649b412d88a60f.rlib" "/opt/rustwide/target/debug/deps/libregex-8578ab2987dde011.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-26bd95c72379fd1e.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-74b2c8a45128fffb.rlib" "/opt/rustwide/target/debug/deps/libucd_util-d37481ea0df54155.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-06b4882bf9bbcddb.rlib" "/opt/rustwide/target/debug/deps/librusty_machine-96bda3760c96b1b5.rlib" "/opt/rustwide/target/debug/deps/librulinalg-bb1e94dc64dcc178.rlib" "/opt/rustwide/target/debug/deps/libnum-9dbba59d754511b6.rlib" "/opt/rustwide/target/debug/deps/libnum_iter-bbf34e9632c3a30c.rlib" "/opt/rustwide/target/debug/deps/libndarray-40e7c17e7a476941.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-7b608b166ebcc1e3.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-a03a7c7129e5b483.rlib" "/opt/rustwide/target/debug/deps/libitertools-fdaa77352c4d66dd.rlib" "/opt/rustwide/target/debug/deps/libapprox-df69f604d5ff4e2e.rlib" "/opt/rustwide/target/debug/deps/librgsl-115f1ec56fa5db3b.rlib" "/opt/rustwide/target/debug/deps/libc_vec-2d25b59c4c33842e.rlib" "/opt/rustwide/target/debug/deps/liblog-1818c57ccc56e23e.rlib" "/opt/rustwide/target/debug/deps/liblog-e50aa4e61ffd3b64.rlib" "/opt/rustwide/target/debug/deps/libcfg_if-da99d89e98e4f9e7.rlib" "/opt/rustwide/target/debug/deps/librust_htslib-a9e224e3f1f60290.rlib" "/opt/rustwide/target/debug/deps/liblzma_sys-dc0de9924a23de5e.rlib" "/opt/rustwide/target/debug/deps/libbzip2_sys-45d273f29764f743.rlib" "/opt/rustwide/target/debug/deps/liblibz_sys-b5aed1669a981fd6.rlib" "/opt/rustwide/target/debug/deps/liblinear_map-dd3c74dbe8a64d8b.rlib" "/opt/rustwide/target/debug/deps/liburl-1b0b9479fbeae824.rlib" "/opt/rustwide/target/debug/deps/libpercent_encoding-fcbc0aacafd7e54d.rlib" "/opt/rustwide/target/debug/deps/libidna-57ce9ee4834dc2dc.rlib" "/opt/rustwide/target/debug/deps/libunicode_normalization-5947cd8ea07dc68c.rlib" "/opt/rustwide/target/debug/deps/libsmallvec-f7a7a9e9ae97b229.rlib" "/opt/rustwide/target/debug/deps/libunicode_bidi-70e078513282caa2.rlib" "/opt/rustwide/target/debug/deps/libmatches-79786252485cca6c.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-1660a65f58d1cb98.rlib" "/opt/rustwide/target/debug/deps/libitertools-9495deec6c4f562f.rlib" "/opt/rustwide/target/debug/deps/libieee754-044555bda52fa77d.rlib" "/opt/rustwide/target/debug/deps/libbitflags-71f40fc9aad530b0.rlib" "/opt/rustwide/target/debug/deps/libbio-cffe87ac54900c91.rlib" "/opt/rustwide/target/debug/deps/libfxhash-4570cd008e269c2c.rlib" "/opt/rustwide/target/debug/deps/libvec_map-9e02dc46b2316171.rlib" "/opt/rustwide/target/debug/deps/libstatrs-50134f548208cce6.rlib" "/opt/rustwide/target/debug/deps/librand-63066fd1042f00bc.rlib" "/opt/rustwide/target/debug/deps/librand-5ae026b052429db3.rlib" "/opt/rustwide/target/debug/deps/libfnv-51dd7c2b44b560c1.rlib" "/opt/rustwide/target/debug/deps/libbv-e4050c55488a9d61.rlib" "/opt/rustwide/target/debug/deps/libordered_float-2bfff96c92c6f830.rlib" "/opt/rustwide/target/debug/deps/libnum_integer-dbac7e428283a153.rlib" "/opt/rustwide/target/debug/deps/libnewtype_derive-9c263ef0a866d441.rlib" "/opt/rustwide/target/debug/deps/libndarray-13ffa6a1adb24eb1.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-f93a5705b17eca85.rlib" "/opt/rustwide/target/debug/deps/libmatrixmultiply-25da71a3fc1835d8.rlib" "/opt/rustwide/target/debug/deps/librawpointer-ad0b02b2fdfa0d4f.rlib" "/opt/rustwide/target/debug/deps/libmultimap-9ca82ea1670115a6.rlib" "/opt/rustwide/target/debug/deps/libitertools_num-a4590234a9482dd0.rlib" "/opt/rustwide/target/debug/deps/libitertools-12e2d7c1acb8bb33.rlib" "/opt/rustwide/target/debug/deps/libeither-bd40eaa39d4ce229.rlib" "/opt/rustwide/target/debug/deps/libcustom_derive-d8dafdd0903c1a8d.rlib" "/opt/rustwide/target/debug/deps/libcsv-588fbb0b141d9665.rlib" "/opt/rustwide/target/debug/deps/libryu-84f5bdeec10241b3.rlib" "/opt/rustwide/target/debug/deps/libitoa-2dfb56471520de1d.rlib" "/opt/rustwide/target/debug/deps/libcsv_core-ddbabcfd337a3b7a.rlib" "/opt/rustwide/target/debug/deps/libbstr-0a885f90fc5b0809.rlib" "/opt/rustwide/target/debug/deps/libregex_automata-fd093be6255b3b91.rlib" "/opt/rustwide/target/debug/deps/libbyteorder-f584045056e081f3.rlib" "/opt/rustwide/target/debug/deps/libbytecount-ddc621fa867848e8.rlib" "/opt/rustwide/target/debug/deps/libbit_set-d3d7dc8cdd637be6.rlib" "/opt/rustwide/target/debug/deps/libbit_vec-449808e879e33fc0.rlib" "/opt/rustwide/target/debug/deps/libapprox-e47a466c3ba6501f.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-a4ff9b7e87bbd905.rlib" "/opt/rustwide/target/debug/deps/libbio_types-9fadca6834a9e9da.rlib" "/opt/rustwide/target/debug/deps/libserde-fe43c0c6b938bd64.rlib" "/opt/rustwide/target/debug/deps/libregex-6dcc6bf681776a04.rlib" "/opt/rustwide/target/debug/deps/libthread_local-708705e5460096e3.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-f17f3dc678462ed0.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-39b017eeb2592fa1.rlib" "/opt/rustwide/target/debug/deps/libmemchr-51469d2f4b469c67.rlib" "/opt/rustwide/target/debug/deps/liblibc-e02979698439167b.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-83cafc2ae303332c.rlib" "/opt/rustwide/target/debug/deps/libquick_error-f5a43a4ceb9b7953.rlib" "-Wl,--start-group" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-12ce12f1efc08aa3.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-5d3cd1b3ddab72e4.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace-f8222943dfd167e2.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace_sys-0cd00b2d3108cd48.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-485c05ba6ce1b438.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-63e6b1072426ba59.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-a421aff1d43911ee.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-3deef8ef4fe80dff.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-f65a176f0586269e.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-ad46d4080f4d7e57.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-da6c590582bf0885.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-837ca740df32db0a.rlib" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-db27c965e824589f.rlib" "-Wl,--end-group" "/opt/rustwide/rustup-home/toolchains/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-68a4f8466685ed76.rlib" "-Wl,-Bdynamic" "-llzma" "-lz" "-lutil" "-lutil" "-ldl" "-lrt" "-lpthread" "-lgcc_s" "-lc" "-lm" "-lrt" "-lpthread" "-lutil" "-lutil" [INFO] [stderr] = note: /opt/rustwide/target/debug/deps/librgsl-115f1ec56fa5db3b.rlib(rgsl-115f1ec56fa5db3b.rgsl.44conf4b-cgu.10.rcgu.o): In function `rgsl::error::erfc': [INFO] [stderr] /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/error.rs:28: undefined reference to `gsl_sf_erfc' [INFO] [stderr] /opt/rustwide/target/debug/deps/librgsl-115f1ec56fa5db3b.rlib(rgsl-115f1ec56fa5db3b.rgsl.44conf4b-cgu.13.rcgu.o): In function `rgsl::randist::gaussian::gaussian_pdf': [INFO] [stderr] /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] [stderr] /opt/rustwide/target/debug/deps/librgsl-115f1ec56fa5db3b.rlib(rgsl-115f1ec56fa5db3b.rgsl.44conf4b-cgu.13.rcgu.o): In function `rgsl::randist::gaussian::ugaussian_P': [INFO] [stderr] /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] [stderr] collect2: error: ld returned 1 exit status [INFO] [stderr] [INFO] [stderr] [INFO] [stderr] error: aborting due to previous error [INFO] [stderr] [INFO] [stderr] error: Could not compile `libprosic`. [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [INFO] running `"docker" "inspect" "d8ac7ee729ff731e82b05836f0e18900a40d4d57ef08f0d7200c68398c6a67e1"` [INFO] running `"docker" "rm" "-f" "d8ac7ee729ff731e82b05836f0e18900a40d4d57ef08f0d7200c68398c6a67e1"` [INFO] [stdout] d8ac7ee729ff731e82b05836f0e18900a40d4d57ef08f0d7200c68398c6a67e1