[INFO] crate varlociraptor 1.1.1 is already in cache [INFO] testing varlociraptor-1.1.1 against beta-2019-09-28 for beta-1.39-1 [INFO] extracting crate varlociraptor 1.1.1 into work/builds/worker-4/source [INFO] validating manifest of crates.io crate varlociraptor 1.1.1 on toolchain beta-2019-09-28 [INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+beta-2019-09-28" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] started tweaking crates.io crate varlociraptor 1.1.1 [INFO] finished tweaking crates.io crate varlociraptor 1.1.1 [INFO] tweaked toml for crates.io crate varlociraptor 1.1.1 written to work/builds/worker-4/source/Cargo.toml [INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+beta-2019-09-28" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+beta-2019-09-28" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-4/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" "+beta-2019-09-28" "build" "--frozen"` [INFO] [stdout] 0e7360a05ab791ce980babfbecabd1a95d24e5a07862692b73c80a30d57e20d5 [INFO] running `"docker" "start" "-a" "0e7360a05ab791ce980babfbecabd1a95d24e5a07862692b73c80a30d57e20d5"` [INFO] [stderr] Compiling memchr v2.2.1 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling yaml-rust v0.3.5 [INFO] [stderr] Compiling rawpointer v0.1.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling bindgen v0.51.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling ucd-trie v0.1.2 [INFO] [stderr] Compiling maplit v1.0.2 [INFO] [stderr] Compiling askama_escape v0.2.0 [INFO] [stderr] Compiling humansize v1.1.0 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling bio v0.28.2 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling strum v0.13.0 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling c_vec v1.0.12 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling custom_error v1.7.1 [INFO] [stderr] Compiling num-complex v0.2.3 [INFO] [stderr] Compiling libz-sys v1.0.25 [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 v0.7.11 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling pest v2.1.2 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling which v3.0.0 [INFO] [stderr] Compiling rustc-hash v1.0.1 [INFO] [stderr] Compiling regex-automata v0.1.8 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling ordered-float v1.0.2 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling counter v0.4.3 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling num v0.1.42 [INFO] [stderr] Compiling vec_map v0.8.1 [INFO] [stderr] Compiling toml v0.4.10 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling serde_yaml v0.8.11 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling eval v0.4.3 [INFO] [stderr] Compiling aho-corasick v0.7.6 [INFO] [stderr] Compiling nom v4.2.3 [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 pest_meta v2.1.2 [INFO] [stderr] Compiling askama_shared v0.8.0 [INFO] [stderr] Compiling cexpr v0.3.5 [INFO] [stderr] Compiling regex v1.3.1 [INFO] [stderr] Compiling csv v1.1.1 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling pest_generator v2.1.1 [INFO] [stderr] Compiling env_logger v0.6.2 [INFO] [stderr] Compiling bio-types v0.5.1 [INFO] [stderr] Compiling bio-types v0.4.0 [INFO] [stderr] Compiling pest_derive v2.1.0 [INFO] [stderr] Compiling darling_core v0.9.0 [INFO] [stderr] Compiling askama_derive v0.8.0 [INFO] [stderr] Compiling strum_macros v0.13.0 [INFO] [stderr] Compiling structopt-derive v0.2.18 [INFO] [stderr] Compiling getset v0.0.7 [INFO] [stderr] Compiling structopt v0.2.18 [INFO] [stderr] Compiling darling_macro v0.9.0 [INFO] [stderr] Compiling darling v0.9.0 [INFO] [stderr] Compiling derive_builder_core v0.5.0 [INFO] [stderr] Compiling derive_builder v0.7.2 [INFO] [stderr] Compiling askama v0.8.0 [INFO] [stderr] Compiling rust-htslib v0.23.0 [INFO] [stderr] Compiling varlociraptor v1.1.1 (/opt/rustwide/workdir) [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call.rs:94:73 [INFO] [stderr] | [INFO] [stderr] 94 | pub fn reference>(self, path: P) -> Result> { [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.rs:100:77 [INFO] [stderr] | [INFO] [stderr] 100 | pub fn inbcf>(self, path: Option

) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call.rs:162:78 [INFO] [stderr] | [INFO] [stderr] 162 | pub fn outbcf>(self, path: Option

) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call.rs:259:46 [INFO] [stderr] | [INFO] [stderr] 259 | pub fn call(&mut self) -> 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/call.rs:283:61 [INFO] [stderr] | [INFO] [stderr] 283 | fn write_call(&mut self, call: &Call) -> 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/call.rs:425:35 [INFO] [stderr] | [INFO] [stderr] 425 | ) -> 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/call_cnvs.rs:63:27 [INFO] [stderr] | [INFO] [stderr] 63 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call_cnvs.rs:154:46 [INFO] [stderr] | [INFO] [stderr] 154 | pub fn call(&mut self) -> 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/call_cnvs.rs:214:36 [INFO] [stderr] | [INFO] [stderr] 214 | let mean_depth = |filter: &Fn(&Call) -> u32| { [INFO] [stderr] | ^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn Fn(&Call) -> u32` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call_cnvs.rs:312:25 [INFO] [stderr] | [INFO] [stderr] 312 | ) -> 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/call_cnvs.rs:533:11 [INFO] [stderr] | [INFO] [stderr] 533 | hmm: &hmm::Model, [INFO] [stderr] | ^^^^^^^^^^^^^ help: use `dyn`: `dyn hmm::Model` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call_cnvs.rs:546:11 [INFO] [stderr] | [INFO] [stderr] 546 | hmm: &hmm::Model, [INFO] [stderr] | ^^^^^^^^^^^^^ help: use `dyn`: `dyn hmm::Model` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call_cnvs.rs:587:70 [INFO] [stderr] | [INFO] [stderr] 587 | pub fn new(record: &mut bcf::Record) -> 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/cli.rs:311:50 [INFO] [stderr] | [INFO] [stderr] 311 | pub fn run(opt: Varlociraptor) -> 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/cli.rs:685:38 [INFO] [stderr] | [INFO] [stderr] 685 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/conversion/decode_phred.rs:9:41 [INFO] [stderr] | [INFO] [stderr] 9 | pub fn decode_phred() -> 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:74:68 [INFO] [stderr] | [INFO] [stderr] 74 | 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:154:33 [INFO] [stderr] | [INFO] [stderr] 154 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/filtration/fdr.rs:40:21 [INFO] [stderr] | [INFO] [stderr] 40 | ) -> 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/filtration/posterior_odds.rs:23:21 [INFO] [stderr] | [INFO] [stderr] 23 | ) -> 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:58:89 [INFO] [stderr] | [INFO] [stderr] 58 | 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:62:68 [INFO] [stderr] | [INFO] [stderr] 62 | 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:143:41 [INFO] [stderr] | [INFO] [stderr] 143 | ) -> 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:37:49 [INFO] [stderr] | [INFO] [stderr] 37 | ) -> 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:77:49 [INFO] [stderr] | [INFO] [stderr] 77 | ) -> 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:123:49 [INFO] [stderr] | [INFO] [stderr] 123 | ) -> 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:214:49 [INFO] [stderr] | [INFO] [stderr] 214 | ) -> 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:77:82 [INFO] [stderr] | [INFO] [stderr] 77 | 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:192:60 [INFO] [stderr] | [INFO] [stderr] 192 | ) -> 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/sample.rs:274:29 [INFO] [stderr] | [INFO] [stderr] 274 | ) -> 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/sample.rs:475:42 [INFO] [stderr] | [INFO] [stderr] 475 | ) -> 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:476:34 [INFO] [stderr] | [INFO] [stderr] 476 | 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:538:42 [INFO] [stderr] | [INFO] [stderr] 538 | ) -> 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:541:44 [INFO] [stderr] | [INFO] [stderr] 541 | -> 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/testcase.rs:75:72 [INFO] [stderr] | [INFO] [stderr] 75 | pub fn reference(self, path: impl AsRef) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/testcase.rs:79:73 [INFO] [stderr] | [INFO] [stderr] 79 | pub fn candidates(self, path: impl AsRef) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/testcase.rs:83:57 [INFO] [stderr] | [INFO] [stderr] 83 | pub fn locus(self, locus: &str) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/testcase.rs:126:60 [INFO] [stderr] | [INFO] [stderr] 126 | fn variants(&mut self) -> 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/testcase.rs:155:47 [INFO] [stderr] | [INFO] [stderr] 155 | pub fn write(&mut self) -> 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:81:46 [INFO] [stderr] | [INFO] [stderr] 81 | ) -> 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:282:62 [INFO] [stderr] | [INFO] [stderr] 282 | 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:310:39 [INFO] [stderr] | [INFO] [stderr] 310 | ) -> 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:363:35 [INFO] [stderr] | [INFO] [stderr] 363 | ) -> 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:407:21 [INFO] [stderr] | [INFO] [stderr] 407 | ) -> 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:436:47 [INFO] [stderr] | [INFO] [stderr] 436 | F: Fn(&mut bcf::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/utils.rs:434:21 [INFO] [stderr] | [INFO] [stderr] 434 | ) -> 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:489:30 [INFO] [stderr] | [INFO] [stderr] 489 | ) -> 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:392:1 [INFO] [stderr] | [INFO] [stderr] 392 | / lazy_static! { [INFO] [stderr] 393 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stderr] 394 | | } [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/likelihood.rs:154:1 [INFO] [stderr] | [INFO] [stderr] 154 | / lazy_static! { [INFO] [stderr] 155 | | static ref PROB_STRAND: LogProb = LogProb(0.5_f64.ln()); [INFO] [stderr] 156 | | } [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] warning: use of deprecated item 'std::sync::ONCE_INIT': the `new` function is now preferred [INFO] [stderr] --> src/testcase.rs:25:1 [INFO] [stderr] | [INFO] [stderr] 25 | / lazy_static! { [INFO] [stderr] 26 | | static ref TESTCASE_RE: Regex = [INFO] [stderr] 27 | | Regex::new(r"^(?P[^:]+):(?P\d+)(:(?P\d+))?$").unwrap(); [INFO] [stderr] 28 | | } [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/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.0.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.1.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.10.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.11.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.12.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.13.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.14.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.15.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.2.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.3.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.4.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.5.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.6.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.7.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.8.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.varlociraptor.f2a2udvz-cgu.9.rcgu.o" "-o" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202" "/opt/rustwide/target/debug/deps/varlociraptor-2bc39af9ce22b202.thq957rpci64m5u.rcgu.o" "-Wl,--gc-sections" "-pie" "-Wl,-zrelro" "-Wl,-znow" "-nodefaultlibs" "-L" "/opt/rustwide/target/debug/deps" "-L" "/opt/rustwide/target/debug/build/rust-htslib-e12f8a1e147458cb/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-e88e5e1390a4bd4f/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/rustwide/target/debug/deps/libfern-828c4a0f6433f18c.rlib" "/opt/rustwide/target/debug/deps/libvarlociraptor-1c5938a2dbe7564f.rlib" "/opt/rustwide/target/debug/deps/libcounter-52997cf632aed83a.rlib" "/opt/rustwide/target/debug/deps/libserde_json-29f99890b391278a.rlib" "/opt/rustwide/target/debug/deps/libbio_types-8f76168d3ce653b0.rlib" "/opt/rustwide/target/debug/deps/libpest-f3f3bc1849d2a601.rlib" "/opt/rustwide/target/debug/deps/libucd_trie-fdcfb289392597aa.rlib" "/opt/rustwide/target/debug/deps/librusty_machine-8595a88b71f61e22.rlib" "/opt/rustwide/target/debug/deps/librulinalg-3f95e525f8e9fd4a.rlib" "/opt/rustwide/target/debug/deps/libnum-b57528460172548f.rlib" "/opt/rustwide/target/debug/deps/libnum_iter-c810663dab3e9f7e.rlib" "/opt/rustwide/target/debug/deps/libcustom_error-82a61a40ce082303.rlib" "/opt/rustwide/target/debug/deps/libserde_yaml-9751365a1f547958.rlib" "/opt/rustwide/target/debug/deps/libdtoa-011d80b1d2654ad7.rlib" "/opt/rustwide/target/debug/deps/libyaml_rust-0f4f6d5c9a50611b.rlib" "/opt/rustwide/target/debug/deps/liblinked_hash_map-f2b67d6ab4d44c07.rlib" "/opt/rustwide/target/debug/deps/librgsl-51feda05c0b72561.rlib" "/opt/rustwide/target/debug/deps/libc_vec-6840fb8c706e6ba8.rlib" "/opt/rustwide/target/debug/deps/librayon-50f13a736df720a0.rlib" "/opt/rustwide/target/debug/deps/librayon_core-c49cf67e7e01c9e7.rlib" "/opt/rustwide/target/debug/deps/libnum_cpus-1c28d23b93f67e46.rlib" "/opt/rustwide/target/debug/deps/libcrossbeam_queue-91a20af24e36b7fc.rlib" "/opt/rustwide/target/debug/deps/libcrossbeam_deque-88cb24a4320751bb.rlib" "/opt/rustwide/target/debug/deps/libcrossbeam_epoch-b354611e19ca8b0a.rlib" "/opt/rustwide/target/debug/deps/libscopeguard-4c52de923eb3c35b.rlib" "/opt/rustwide/target/debug/deps/libmemoffset-0a15f9717a13ff60.rlib" "/opt/rustwide/target/debug/deps/libcrossbeam_utils-b01e92d2daf9a708.rlib" "/opt/rustwide/target/debug/deps/libarrayvec-d208b7397580726a.rlib" "/opt/rustwide/target/debug/deps/libnodrop-2429cd2ceac458fc.rlib" "/opt/rustwide/target/debug/deps/librust_htslib-0c4a08cb80a306bb.rlib" "/opt/rustwide/target/debug/deps/liblzma_sys-1839fef4ef3dcb9e.rlib" "/opt/rustwide/target/debug/deps/libbzip2_sys-c1f891b36aeba473.rlib" "/opt/rustwide/target/debug/deps/liblibz_sys-57eb44a08d8c5ab5.rlib" "/opt/rustwide/target/debug/deps/liblinear_map-58376a02dfe71761.rlib" "/opt/rustwide/target/debug/deps/liburl-a72a174ec3a5c69b.rlib" "/opt/rustwide/target/debug/deps/libpercent_encoding-24177bf8e4a597fd.rlib" "/opt/rustwide/target/debug/deps/libidna-045d1ae9b0112dc5.rlib" "/opt/rustwide/target/debug/deps/libunicode_normalization-c65379e9aa11b52d.rlib" "/opt/rustwide/target/debug/deps/libsmallvec-a6ff3ddf243f392a.rlib" "/opt/rustwide/target/debug/deps/libunicode_bidi-5b064f932e6646ad.rlib" "/opt/rustwide/target/debug/deps/libmatches-25f72eb55a371331.rlib" "/opt/rustwide/target/debug/deps/libieee754-97aa23e724f660bd.rlib" "/opt/rustwide/target/debug/deps/libbitflags-920bcd2eac591960.rlib" "/opt/rustwide/target/debug/deps/libitertools-c752445a97406995.rlib" "/opt/rustwide/target/debug/deps/libbio-521767cde113aa97.rlib" "/opt/rustwide/target/debug/deps/libstrum-eaa972d1ab99eb63.rlib" "/opt/rustwide/target/debug/deps/libitertools_num-4d0b74c53a142160.rlib" "/opt/rustwide/target/debug/deps/libstatrs-d4a5b0cb9ee8526c.rlib" "/opt/rustwide/target/debug/deps/librand-25aea7435ca545a1.rlib" "/opt/rustwide/target/debug/deps/librand-a866ea5e4ea209cb.rlib" "/opt/rustwide/target/debug/deps/libordered_float-c76da1f51f9731b0.rlib" "/opt/rustwide/target/debug/deps/libndarray-057cd3a1409ddf69.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-2bfbb2133dc12204.rlib" "/opt/rustwide/target/debug/deps/libmatrixmultiply-52e0ac25033cd383.rlib" "/opt/rustwide/target/debug/deps/librawpointer-9eec285a84ee4032.rlib" "/opt/rustwide/target/debug/deps/libmultimap-f11878586df28cbd.rlib" "/opt/rustwide/target/debug/deps/libitertools-57b1f43b793c2f74.rlib" "/opt/rustwide/target/debug/deps/libeither-a375c15081516f4e.rlib" "/opt/rustwide/target/debug/deps/libcsv-7641ceda4004d15c.rlib" "/opt/rustwide/target/debug/deps/libryu-6dbb2e6f31cf0558.rlib" "/opt/rustwide/target/debug/deps/libitoa-e736842aeff4074b.rlib" "/opt/rustwide/target/debug/deps/libcsv_core-e09054852c0dd71f.rlib" "/opt/rustwide/target/debug/deps/libbstr-ec5cf33d14496ed0.rlib" "/opt/rustwide/target/debug/deps/libregex_automata-0293950fd499c502.rlib" "/opt/rustwide/target/debug/deps/libnum_integer-2dd52f0ea276c9ff.rlib" "/opt/rustwide/target/debug/deps/libbv-c6cf8fe3584dd2a5.rlib" "/opt/rustwide/target/debug/deps/libbytecount-87f025bdcf811407.rlib" "/opt/rustwide/target/debug/deps/libbit_set-e831679a86d1ec23.rlib" "/opt/rustwide/target/debug/deps/libbit_vec-223fe1d81301185c.rlib" "/opt/rustwide/target/debug/deps/libbio_types-70bfd7d9e9e1b83a.rlib" "/opt/rustwide/target/debug/deps/libregex-44cca58b69f05d73.rlib" "/opt/rustwide/target/debug/deps/libthread_local-476b4cfeb59ceacc.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-641806fdaa87370c.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-42dcf61e41c16151.rlib" "/opt/rustwide/target/debug/deps/libmemchr-1e96e25872fe69aa.rlib" "/opt/rustwide/target/debug/deps/libfxhash-6c59c41fea9e8ddd.rlib" "/opt/rustwide/target/debug/deps/libbyteorder-fdd43a3ae319d8ce.rlib" "/opt/rustwide/target/debug/deps/libpetgraph-2169043aeccdf72d.rlib" "/opt/rustwide/target/debug/deps/libordermap-7c6aebc286cc0c26.rlib" "/opt/rustwide/target/debug/deps/libfixedbitset-77277783c273097f.rlib" "/opt/rustwide/target/debug/deps/libnewtype_derive-635c713e349bdbd4.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-955d54352a795d1f.rlib" "/opt/rustwide/target/debug/deps/libcustom_derive-1a26498bf02af92d.rlib" "/opt/rustwide/target/debug/deps/libaskama-b3fd70015c50477c.rlib" "/opt/rustwide/target/debug/deps/libaskama_shared-e145dd2a6655d0bb.rlib" "/opt/rustwide/target/debug/deps/libhumansize-8a4f43841bb0a5ad.rlib" "/opt/rustwide/target/debug/deps/libaskama_escape-3baaa7a866e4c85e.rlib" "/opt/rustwide/target/debug/deps/libtoml-db6abf2f7705ed7c.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-47d24117de3918be.rlib" "/opt/rustwide/target/debug/deps/libquick_error-9411b7aab885de58.rlib" "/opt/rustwide/target/debug/deps/libapprox-46427b9d8127f102.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-a49361b936b25068.rlib" "/opt/rustwide/target/debug/deps/liblog-03e85f8c88e058b0.rlib" "/opt/rustwide/target/debug/deps/liblog-5513cb556299afcf.rlib" "/opt/rustwide/target/debug/deps/libcfg_if-1e2186a891f602d1.rlib" "/opt/rustwide/target/debug/deps/libstructopt-4756c2bc91f15751.rlib" "/opt/rustwide/target/debug/deps/libclap-c71e894b66e54e46.rlib" "/opt/rustwide/target/debug/deps/libyaml_rust-b0070dd56b05e81e.rlib" "/opt/rustwide/target/debug/deps/libvec_map-b88c7842e4422229.rlib" "/opt/rustwide/target/debug/deps/libserde-7b151d47f3e0e035.rlib" "/opt/rustwide/target/debug/deps/libtextwrap-1f2d63b65184cfac.rlib" "/opt/rustwide/target/debug/deps/libunicode_width-b9c8816a90102d04.rlib" "/opt/rustwide/target/debug/deps/libstrsim-ec36f8fc183413c4.rlib" "/opt/rustwide/target/debug/deps/libbitflags-4961bb5087b14aca.rlib" "/opt/rustwide/target/debug/deps/libatty-03b8a93222186773.rlib" "/opt/rustwide/target/debug/deps/liblibc-9f7a5de25bd5699b.rlib" "/opt/rustwide/target/debug/deps/libansi_term-d783327a58311329.rlib" "-Wl,--start-group" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-db812c66f862af4c.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-e7871a21575d5ff7.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-2f2c581bc0d759e6.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-35731cabc05dc8a0.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace-36477394541292db.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace_sys-8b706b170c1272d8.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-801dbb3043ccf581.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-a32aa66ce6f72b21.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-d00ea3bfb2bb6c00.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-d2c6ebe88c3e113c.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-df74f62f6bb60621.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-2170473575daeedb.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-1a08089bbddc4f51.rlib" "-Wl,--end-group" "/opt/rustwide/rustup-home/toolchains/beta-2019-09-28-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-f8f562e5472ad5c3.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-51feda05c0b72561.rlib(rgsl-51feda05c0b72561.rgsl.dpigxrc8-cgu.13.rcgu.o): In function `rgsl::randist::binomial::binomial_pdf': [INFO] [stderr] /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/randist/binomial.rs:19: undefined reference to `gsl_ran_binomial_pdf' [INFO] [stderr] /opt/rustwide/target/debug/deps/librgsl-51feda05c0b72561.rlib(rgsl-51feda05c0b72561.rgsl.dpigxrc8-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] /opt/rustwide/target/debug/deps/librgsl-51feda05c0b72561.rlib(rgsl-51feda05c0b72561.rgsl.dpigxrc8-cgu.6.rcgu.o): In function `rgsl::randist::poisson::poisson_pdf': [INFO] [stderr] /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/randist/poisson.rs:19: undefined reference to `gsl_ran_poisson_pdf' [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 `varlociraptor`. [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [INFO] running `"docker" "inspect" "0e7360a05ab791ce980babfbecabd1a95d24e5a07862692b73c80a30d57e20d5"` [INFO] running `"docker" "rm" "-f" "0e7360a05ab791ce980babfbecabd1a95d24e5a07862692b73c80a30d57e20d5"` [INFO] [stdout] 0e7360a05ab791ce980babfbecabd1a95d24e5a07862692b73c80a30d57e20d5