[INFO] crate libprosic 0.7.3 is already in cache [INFO] testing libprosic-0.7.3 against try#41997647ba6a77908f6ef64401414feb00bccf16 for pr-71274 [INFO] extracting crate libprosic 0.7.3 into /workspace/builds/worker-7/source [INFO] validating manifest of crates.io crate libprosic 0.7.3 on toolchain 41997647ba6a77908f6ef64401414feb00bccf16 [INFO] running `"/workspace/cargo-home/bin/cargo" "+41997647ba6a77908f6ef64401414feb00bccf16" "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 /workspace/builds/worker-7/source/Cargo.toml [INFO] running `"/workspace/cargo-home/bin/cargo" "+41997647ba6a77908f6ef64401414feb00bccf16" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/workspace/cargo-home/bin/cargo" "+41997647ba6a77908f6ef64401414feb00bccf16" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/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=forbid" "-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" "+41997647ba6a77908f6ef64401414feb00bccf16" "build" "--frozen"` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] b085482d6b2064262f76078f719354539ca5a6eeb6f74a06ee93b6bf998f2800 [INFO] running `"docker" "start" "-a" "b085482d6b2064262f76078f719354539ca5a6eeb6f74a06ee93b6bf998f2800"` [INFO] [stderr] Compiling libc v0.2.69 [INFO] [stderr] Compiling autocfg v1.0.0 [INFO] [stderr] Compiling proc-macro2 v1.0.10 [INFO] [stderr] Compiling unicode-xid v0.2.0 [INFO] [stderr] Compiling cc v1.0.50 [INFO] [stderr] Compiling memchr v2.3.3 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling pkg-config v0.3.17 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling regex-syntax v0.6.17 [INFO] [stderr] Compiling glob v0.2.11 [INFO] [stderr] Compiling log v0.4.8 [INFO] [stderr] Compiling cfg-if v0.1.10 [INFO] [stderr] Compiling either v1.5.3 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling ucd-util v0.1.8 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling unicode-width v0.1.7 [INFO] [stderr] Compiling rawpointer v0.1.0 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling utf8-ranges v1.0.4 [INFO] [stderr] Compiling termcolor v1.1.0 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling ryu v1.0.3 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling smallvec v1.3.0 [INFO] [stderr] Compiling matches v0.1.8 [INFO] [stderr] Compiling peeking_take_while v0.1.2 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling fnv v1.0.6 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling lazy_static v0.2.11 [INFO] [stderr] Compiling c_vec v1.0.12 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling thread_local v1.0.1 [INFO] [stderr] Compiling thread_local v0.3.6 [INFO] [stderr] Compiling humantime v1.3.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling itertools v0.7.11 [INFO] [stderr] Compiling itertools v0.6.5 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling num-traits v0.2.11 [INFO] [stderr] Compiling num-integer v0.1.42 [INFO] [stderr] Compiling num-iter v0.1.40 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling regex-syntax v0.5.6 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling proc-macro2 v0.3.5 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling unicode-bidi v0.3.4 [INFO] [stderr] Compiling unicode-normalization v0.1.12 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling libloading v0.5.2 [INFO] [stderr] Compiling bzip2-sys v0.1.8+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.15 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling quote v0.5.2 [INFO] [stderr] Compiling aho-corasick v0.7.10 [INFO] [stderr] Compiling aho-corasick v0.6.10 [INFO] [stderr] Compiling csv-core v0.1.10 [INFO] [stderr] Compiling log v0.3.9 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling quote v1.0.3 [INFO] [stderr] Compiling idna v0.1.5 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Compiling rand v0.4.6 [INFO] [stderr] Compiling syn v1.0.17 [INFO] [stderr] Compiling nom v3.2.1 [INFO] [stderr] Compiling regex v1.3.7 [INFO] [stderr] Compiling url v1.7.2 [INFO] [stderr] Compiling num-traits v0.1.43 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling ordered-float v1.0.2 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling rand v0.3.23 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling num v0.1.42 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling serde_derive v1.0.106 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling serde v1.0.106 [INFO] [stderr] Compiling vec_map v0.8.1 [INFO] [stderr] Compiling bio-types v0.6.0 [INFO] [stderr] Compiling bstr v0.2.12 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling clap v2.33.0 [INFO] [stderr] Compiling csv v1.1.3 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:62:20 [INFO] [stderr] | [INFO] [stderr] 62 | let variants = try!(utils::collect_variants( [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(deprecated)]` on by default [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:70:21 [INFO] [stderr] | [INFO] [stderr] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:75:18 [INFO] [stderr] | [INFO] [stderr] 75 | Some(try!(joint_model.pileup( [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:159:26 [INFO] [stderr] | [INFO] [stderr] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/model/sample.rs:76:17 [INFO] [stderr] | [INFO] [stderr] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stderr] | ^^^ [INFO] [stderr] [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: this warning originates in a macro (in Nightly builds, run with -Z 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 (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: 33 warnings emitted [INFO] [stderr] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 3m 44s [INFO] running `"docker" "inspect" "b085482d6b2064262f76078f719354539ca5a6eeb6f74a06ee93b6bf998f2800"` [INFO] running `"docker" "rm" "-f" "b085482d6b2064262f76078f719354539ca5a6eeb6f74a06ee93b6bf998f2800"` [INFO] [stdout] b085482d6b2064262f76078f719354539ca5a6eeb6f74a06ee93b6bf998f2800 [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/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=forbid" "-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" "+41997647ba6a77908f6ef64401414feb00bccf16" "test" "--frozen" "--no-run"` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] d72d91413a69cab6f6b94a85745119f5a7fd57e89e9cc2df854e5f2bfacdb49d [INFO] running `"docker" "start" "-a" "d72d91413a69cab6f6b94a85745119f5a7fd57e89e9cc2df854e5f2bfacdb49d"` [INFO] [stderr] Compiling version_check v0.1.5 [INFO] [stderr] Compiling regex-syntax v0.3.9 [INFO] [stderr] Compiling utf8-ranges v0.1.3 [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling memchr v0.1.11 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling time v0.1.42 [INFO] [stderr] Compiling base64 v0.9.3 [INFO] [stderr] Compiling mime v0.2.6 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] Compiling aho-corasick v0.5.3 [INFO] [stderr] Compiling thread-id v2.0.0 [INFO] [stderr] Compiling unicase v1.4.2 [INFO] [stderr] Compiling thread_local v0.2.7 [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:62:20 [INFO] [stderr] | [INFO] [stderr] 62 | let variants = try!(utils::collect_variants( [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(deprecated)]` on by default [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:70:21 [INFO] [stderr] | [INFO] [stderr] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:75:18 [INFO] [stderr] | [INFO] [stderr] 75 | Some(try!(joint_model.pileup( [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:159:26 [INFO] [stderr] | [INFO] [stderr] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/model/sample.rs:76:17 [INFO] [stderr] | [INFO] [stderr] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stderr] | ^^^ [INFO] [stderr] [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: this warning originates in a macro (in Nightly builds, run with -Z 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 (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: 33 warnings emitted [INFO] [stderr] [INFO] [stderr] Compiling flate2 v0.2.20 [INFO] [stderr] Compiling hyper v0.10.16 [INFO] [stderr] Compiling regex v0.1.80 [INFO] [stderr] Compiling env_logger v0.3.5 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:62:20 [INFO] [stderr] | [INFO] [stderr] 62 | let variants = try!(utils::collect_variants( [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(deprecated)]` on by default [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:70:21 [INFO] [stderr] | [INFO] [stderr] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:75:18 [INFO] [stderr] | [INFO] [stderr] 75 | Some(try!(joint_model.pileup( [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:159:26 [INFO] [stderr] | [INFO] [stderr] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/model/sample.rs:76:17 [INFO] [stderr] | [INFO] [stderr] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stderr] | ^^^ [INFO] [stderr] [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: this warning originates in a macro (in Nightly builds, run with -Z 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 (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] 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] [stderr] --> src/model/sample.rs:612:79 [INFO] [stderr] | [INFO] [stderr] 612 | for (record, true_alt_prob) in records.into_iter().zip(true_alt_probs.into_iter()) { [INFO] [stderr] | ^^^^^^^^^ help: use `.iter()` instead of `.into_iter()` to avoid ambiguity: `iter` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(array_into_iter)]` on by default [INFO] [stderr] = warning: this was previously accepted by the compiler but is being phased out; it will become a hard error in a future release! [INFO] [stderr] = note: for more information, see issue #66145 [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/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.0.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.1.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.10.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.11.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.12.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.13.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.14.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.15.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.2.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.3.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.4.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.5.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.6.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.7.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.8.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.libprosic.79g7qr7x-cgu.9.rcgu.o" "-o" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5" "/opt/rustwide/target/debug/deps/libprosic-b92235f53bd283b5.yjg999fq6i3v3t1.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-521308dcba8657ad/out" "-L" "/opt/rustwide/target/debug/build/rust-htslib-24f3ebb93b2d4718/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-552e210a8746ad91/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libtest-a6274e2eaafd361e.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libterm-2c85f64fb49c1603.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgetopts-ed84df1a106a13ed.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunicode_width-e159833bdb71170b.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_std-5f1c8c824853fda4.rlib" "/opt/rustwide/target/debug/deps/libenv_logger-f67333ac94cedadd.rlib" "/opt/rustwide/target/debug/deps/libregex-e9b70bcfd47a102f.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-1b60f528dd4155d9.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-00bcdd374c605b4a.rlib" "/opt/rustwide/target/debug/deps/libthread_local-2a97ec0f3be9e3cf.rlib" "/opt/rustwide/target/debug/deps/libthread_id-9450cb663aad5933.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-0388c9831b26f5fc.rlib" "/opt/rustwide/target/debug/deps/libmemchr-d00cbe9e629133a2.rlib" "/opt/rustwide/target/debug/deps/libcached-db0e10328fbba1d9.rlib" "/opt/rustwide/target/debug/deps/libregex-968aa111634235c8.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-73b9a414549369b7.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-4a3485cc8b2de090.rlib" "/opt/rustwide/target/debug/deps/libucd_util-2cad64ef0548d015.rlib" "/opt/rustwide/target/debug/deps/libthread_local-54c5a590687748e9.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-37a3566ce068430c.rlib" "/opt/rustwide/target/debug/deps/librusty_machine-2b5a52e4a0a279c1.rlib" "/opt/rustwide/target/debug/deps/librulinalg-1ccb46fdd52feadd.rlib" "/opt/rustwide/target/debug/deps/libnum-65d486bcc34c565f.rlib" "/opt/rustwide/target/debug/deps/libnum_iter-a9121b727fa3a111.rlib" "/opt/rustwide/target/debug/deps/libndarray-c3ff0b0ca1559386.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-171a6f2775c32e9b.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-9db42f54d151e0f2.rlib" "/opt/rustwide/target/debug/deps/libitertools-6cd2f51328fc52c6.rlib" "/opt/rustwide/target/debug/deps/libapprox-14b892f25d2a8baa.rlib" "/opt/rustwide/target/debug/deps/librgsl-61903f5054c38bd9.rlib" "/opt/rustwide/target/debug/deps/libc_vec-51159ab0c7c1eab1.rlib" "/opt/rustwide/target/debug/deps/liblog-bd3d795ce9bbd9ff.rlib" "/opt/rustwide/target/debug/deps/liblog-e05329b9ca199b2b.rlib" "/opt/rustwide/target/debug/deps/libcfg_if-7bfa6ddb9b2ff1d3.rlib" "/opt/rustwide/target/debug/deps/librust_htslib-e411c72ee8dad32d.rlib" "/opt/rustwide/target/debug/deps/liblzma_sys-b6feb356b0e39c3c.rlib" "/opt/rustwide/target/debug/deps/libbzip2_sys-8bdad7567e8530ca.rlib" "/opt/rustwide/target/debug/deps/liblibz_sys-fbaeb05fb739282d.rlib" "/opt/rustwide/target/debug/deps/liblinear_map-53dd41e525d82bd8.rlib" "/opt/rustwide/target/debug/deps/liburl-85f5b3d67989c8bb.rlib" "/opt/rustwide/target/debug/deps/libpercent_encoding-e56e189c1cd50c76.rlib" "/opt/rustwide/target/debug/deps/libidna-63ecf49c816f6752.rlib" "/opt/rustwide/target/debug/deps/libunicode_normalization-fb934dbb15c42074.rlib" "/opt/rustwide/target/debug/deps/libsmallvec-079a3bb21ce585fc.rlib" "/opt/rustwide/target/debug/deps/libunicode_bidi-5e81168a03bf27b8.rlib" "/opt/rustwide/target/debug/deps/libmatches-9b2fa40a52aed94f.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-26a3a548d6bb9511.rlib" "/opt/rustwide/target/debug/deps/libitertools-a2b996669fb48b66.rlib" "/opt/rustwide/target/debug/deps/libieee754-4b24baea288cd36c.rlib" "/opt/rustwide/target/debug/deps/libbitflags-1b60fd1bab4fdb80.rlib" "/opt/rustwide/target/debug/deps/libbio-57e1ad270ea2232d.rlib" "/opt/rustwide/target/debug/deps/libfxhash-66b8caf7bb47bcd8.rlib" "/opt/rustwide/target/debug/deps/libvec_map-fd674fe55fd9d8c3.rlib" "/opt/rustwide/target/debug/deps/libstatrs-8139765cd5d90392.rlib" "/opt/rustwide/target/debug/deps/librand-bf0770608bdf33e8.rlib" "/opt/rustwide/target/debug/deps/librand-c8ebfe8e76a6e3d0.rlib" "/opt/rustwide/target/debug/deps/liblibc-abf87f40fd2d9d6d.rlib" "/opt/rustwide/target/debug/deps/libfnv-5eb3a865ee06cdd3.rlib" "/opt/rustwide/target/debug/deps/libbv-2a63a4f4eace864f.rlib" "/opt/rustwide/target/debug/deps/libordered_float-47d9feafc4d3f559.rlib" "/opt/rustwide/target/debug/deps/libnum_integer-9032d7a2d99629ef.rlib" "/opt/rustwide/target/debug/deps/libnewtype_derive-8bf230b860a8a9cf.rlib" "/opt/rustwide/target/debug/deps/libndarray-cb613661712fbc4f.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-623ec6308ee20876.rlib" "/opt/rustwide/target/debug/deps/libmatrixmultiply-4596ec347f169968.rlib" "/opt/rustwide/target/debug/deps/librawpointer-8511a3c6951f373b.rlib" "/opt/rustwide/target/debug/deps/libmultimap-2e32ea26ed4f686c.rlib" "/opt/rustwide/target/debug/deps/libitertools_num-d5c405d337d811bd.rlib" "/opt/rustwide/target/debug/deps/libitertools-5317c1d3a22625c4.rlib" "/opt/rustwide/target/debug/deps/libeither-f74d019d6d596424.rlib" "/opt/rustwide/target/debug/deps/libcustom_derive-ce521f9361401a80.rlib" "/opt/rustwide/target/debug/deps/libcsv-74f41ae4ffa7363c.rlib" "/opt/rustwide/target/debug/deps/libryu-12d8e5edf3ac1d84.rlib" "/opt/rustwide/target/debug/deps/libitoa-2a0f8bb85d8127c5.rlib" "/opt/rustwide/target/debug/deps/libcsv_core-722a374f275f6ee9.rlib" "/opt/rustwide/target/debug/deps/libbstr-eb1e978b51e73e53.rlib" "/opt/rustwide/target/debug/deps/libregex_automata-fd8651c83b6fc95b.rlib" "/opt/rustwide/target/debug/deps/libbyteorder-7b8e532639ee0fad.rlib" "/opt/rustwide/target/debug/deps/libbytecount-53c83cceb29c28ff.rlib" "/opt/rustwide/target/debug/deps/libbit_set-f2b3427e4674fbf5.rlib" "/opt/rustwide/target/debug/deps/libbit_vec-6e7b2bc5b42e5ad2.rlib" "/opt/rustwide/target/debug/deps/libapprox-30c82bc26fc6cf09.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-9f97a4fd61bd1e10.rlib" "/opt/rustwide/target/debug/deps/libbio_types-e8555a9400b9469a.rlib" "/opt/rustwide/target/debug/deps/libserde-d0fa92bf6b671f35.rlib" "/opt/rustwide/target/debug/deps/libregex-5673d2c692486c34.rlib" "/opt/rustwide/target/debug/deps/libthread_local-99a05dc3a68e4d67.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-895f7b6116abae12.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-171112384f1bc6b1.rlib" "/opt/rustwide/target/debug/deps/libmemchr-e6743c7b9c8d789f.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-81e71b56f2a8a8f3.rlib" "/opt/rustwide/target/debug/deps/libquick_error-c339d616bf8720e1.rlib" "-Wl,--start-group" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-62f93208e14fa8f0.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-b2c4dbe979cef5e2.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-8b9b66cb3e9f891d.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-5998b08bf29f56ac.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace-efd1670396ccb585.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace_sys-6435b9209e888961.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-866e5dfb603b34d2.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-75eac3089695b3b4.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-35744537b4825584.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-f7ee5081d96fb2cd.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-5b28479cb639d76c.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-f827473dd3b319fa.rlib" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-53f9c299c549c6a9.rlib" "-Wl,--end-group" "/opt/rustwide/rustup-home/toolchains/41997647ba6a77908f6ef64401414feb00bccf16/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-44132fbb3fcc18d3.rlib" "-Wl,-Bdynamic" "-llzma" "-lz" "-lutil" "-ldl" "-lutil" "-ldl" "-lrt" "-lpthread" "-lgcc_s" "-lc" "-lm" "-lrt" "-lpthread" "-lutil" "-ldl" "-lutil" [INFO] [stderr] = note: /opt/rustwide/target/debug/deps/librgsl-61903f5054c38bd9.rlib(rgsl-61903f5054c38bd9.rgsl.3aqvz9bq-cgu.11.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-61903f5054c38bd9.rlib(rgsl-61903f5054c38bd9.rgsl.3aqvz9bq-cgu.11.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] /opt/rustwide/target/debug/deps/librgsl-61903f5054c38bd9.rlib(rgsl-61903f5054c38bd9.rgsl.3aqvz9bq-cgu.9.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] collect2: error: ld returned 1 exit status [INFO] [stderr] [INFO] [stderr] [INFO] [stderr] error: aborting due to previous error; 34 warnings emitted [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" "d72d91413a69cab6f6b94a85745119f5a7fd57e89e9cc2df854e5f2bfacdb49d"` [INFO] running `"docker" "rm" "-f" "d72d91413a69cab6f6b94a85745119f5a7fd57e89e9cc2df854e5f2bfacdb49d"` [INFO] [stdout] d72d91413a69cab6f6b94a85745119f5a7fd57e89e9cc2df854e5f2bfacdb49d