[INFO] crate varlociraptor 1.1.1 is already in cache [INFO] testing varlociraptor-1.1.1 against 1.38.0 for beta-1.39-1 [INFO] extracting crate varlociraptor 1.1.1 into work/builds/worker-5/source [INFO] validating manifest of crates.io crate varlociraptor 1.1.1 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 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-5/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] running `"/big/crater/work/cargo-home/bin/cargo" "+1.38.0" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-5/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] f3c09c29f00219d79dcc94bcd5809b7b6d409e356eafc0d8b89b69fd168a4bc9 [INFO] running `"docker" "start" "-a" "f3c09c29f00219d79dcc94bcd5809b7b6d409e356eafc0d8b89b69fd168a4bc9"` [INFO] [stderr] Compiling memchr v2.2.1 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling bindgen v0.51.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling humansize v1.1.0 [INFO] [stderr] Compiling askama_escape v0.2.0 [INFO] [stderr] Compiling bio v0.28.2 [INFO] [stderr] Compiling bit-vec v0.5.1 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling c_vec v1.0.12 [INFO] [stderr] Compiling strum v0.13.0 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling custom_error v1.7.1 [INFO] [stderr] Compiling bzip2-sys v0.1.7 [INFO] [stderr] Compiling fs-utils v1.1.1 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Compiling lzma-sys v0.1.15 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling itertools v0.7.11 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling newtype_derive v0.1.6 [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 bit-set v0.5.1 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling ordered-float v1.0.2 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling counter v0.4.3 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling pest_generator v2.1.1 [INFO] [stderr] Compiling derive-new v0.5.8 [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 serde_yaml v0.8.11 [INFO] [stderr] Compiling askama_shared v0.8.0 [INFO] [stderr] Compiling eval v0.4.3 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling clap v2.33.0 [INFO] [stderr] Compiling aho-corasick v0.7.6 [INFO] [stderr] Compiling nom v4.2.3 [INFO] [stderr] Compiling bstr v0.2.8 [INFO] [stderr] Compiling csv-core v0.1.6 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling csv v1.1.1 [INFO] [stderr] Compiling regex v1.3.1 [INFO] [stderr] Compiling cexpr v0.3.5 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling pest_derive v2.1.0 [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 darling_core v0.9.0 [INFO] [stderr] Compiling strum_macros v0.13.0 [INFO] [stderr] Compiling askama_derive v0.8.0 [INFO] [stderr] Compiling structopt-derive v0.2.18 [INFO] [stderr] Compiling getset v0.0.7 [INFO] [stderr] Compiling darling_macro v0.9.0 [INFO] [stderr] Compiling structopt v0.2.18 [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 rust-htslib v0.23.0 [INFO] [stderr] Compiling askama v0.8.0 [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/1.38.0-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.0.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.1.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.10.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.11.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.12.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.13.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.14.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.15.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.2.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.3.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.4.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.5.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.6.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.7.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.8.rcgu.o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.varlociraptor.3ofuu7q8-cgu.9.rcgu.o" "-o" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5" "/opt/rustwide/target/debug/deps/varlociraptor-518da212ddc69ea5.7x8fieh5thj8y48.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-3aa9942db28b0d60/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/target/debug/deps/libfern-bf5f478b959d8cce.rlib" "/opt/rustwide/target/debug/deps/libvarlociraptor-34009f0564725df0.rlib" "/opt/rustwide/target/debug/deps/libcounter-3edf5627e5ed1365.rlib" "/opt/rustwide/target/debug/deps/libserde_json-90f598e0640daaf7.rlib" "/opt/rustwide/target/debug/deps/libbio_types-fd95f209a8f6bdd6.rlib" "/opt/rustwide/target/debug/deps/libpest-2e4fa98b48d08e81.rlib" "/opt/rustwide/target/debug/deps/libucd_trie-d5ea503f523492b8.rlib" "/opt/rustwide/target/debug/deps/librusty_machine-c1ad8164e1fa52a7.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/libcustom_error-b93b1f46f6fbcbb6.rlib" "/opt/rustwide/target/debug/deps/libserde_yaml-3a6ad8eb990c1094.rlib" "/opt/rustwide/target/debug/deps/libdtoa-2d9163607197f742.rlib" "/opt/rustwide/target/debug/deps/libyaml_rust-601ebb2bb0e6056b.rlib" "/opt/rustwide/target/debug/deps/liblinked_hash_map-91e14c801aea6c1e.rlib" "/opt/rustwide/target/debug/deps/librgsl-aea97a06a6f5704e.rlib" "/opt/rustwide/target/debug/deps/libc_vec-2d25b59c4c33842e.rlib" "/opt/rustwide/target/debug/deps/librayon-f5a934ab03b6a946.rlib" "/opt/rustwide/target/debug/deps/librayon_core-7f0491299ed48e0b.rlib" "/opt/rustwide/target/debug/deps/libnum_cpus-1a9b896f537e17c6.rlib" "/opt/rustwide/target/debug/deps/libcrossbeam_queue-03e303f785e3b31c.rlib" "/opt/rustwide/target/debug/deps/libcrossbeam_deque-72254c766af146f6.rlib" "/opt/rustwide/target/debug/deps/libcrossbeam_epoch-68d059ccc210e9ef.rlib" "/opt/rustwide/target/debug/deps/libscopeguard-b65f244d92643e92.rlib" "/opt/rustwide/target/debug/deps/libmemoffset-7995e17cac3528a2.rlib" "/opt/rustwide/target/debug/deps/libcrossbeam_utils-cab10adef0565ac1.rlib" "/opt/rustwide/target/debug/deps/libarrayvec-5e2034b2a5a9087d.rlib" "/opt/rustwide/target/debug/deps/libnodrop-5afc3432f0530b99.rlib" "/opt/rustwide/target/debug/deps/librust_htslib-b41ee3d7cb76e534.rlib" "/opt/rustwide/target/debug/deps/liblzma_sys-17de1574cfd80163.rlib" "/opt/rustwide/target/debug/deps/libbzip2_sys-7a16deecd71ffaf2.rlib" "/opt/rustwide/target/debug/deps/liblibz_sys-71c88e1c4ac26ee0.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/libieee754-044555bda52fa77d.rlib" "/opt/rustwide/target/debug/deps/libbitflags-71f40fc9aad530b0.rlib" "/opt/rustwide/target/debug/deps/libitertools-4c15bcc5211318bc.rlib" "/opt/rustwide/target/debug/deps/libbio-24a656a8e229c7d1.rlib" "/opt/rustwide/target/debug/deps/libstrum-ecb3ce1e26a7f669.rlib" "/opt/rustwide/target/debug/deps/libitertools_num-a4590234a9482dd0.rlib" "/opt/rustwide/target/debug/deps/libstatrs-a396cacdbd8dcbc9.rlib" "/opt/rustwide/target/debug/deps/librand-df37cf038f4c3201.rlib" "/opt/rustwide/target/debug/deps/librand-250eafcf18e8ca2a.rlib" "/opt/rustwide/target/debug/deps/libordered_float-2bfff96c92c6f830.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-12e2d7c1acb8bb33.rlib" "/opt/rustwide/target/debug/deps/libeither-bd40eaa39d4ce229.rlib" "/opt/rustwide/target/debug/deps/libcsv-4cd661b8736a7443.rlib" "/opt/rustwide/target/debug/deps/libryu-84f5bdeec10241b3.rlib" "/opt/rustwide/target/debug/deps/libitoa-2dfb56471520de1d.rlib" "/opt/rustwide/target/debug/deps/libcsv_core-105793b84c261a1a.rlib" "/opt/rustwide/target/debug/deps/libbstr-49285489500a2c16.rlib" "/opt/rustwide/target/debug/deps/libregex_automata-fd093be6255b3b91.rlib" "/opt/rustwide/target/debug/deps/libnum_integer-dbac7e428283a153.rlib" "/opt/rustwide/target/debug/deps/libbv-e4050c55488a9d61.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/libbio_types-0995771d88f756f4.rlib" "/opt/rustwide/target/debug/deps/libregex-d9487fb83d9279e4.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-2d69d411c6e31321.rlib" "/opt/rustwide/target/debug/deps/libmemchr-24d7c0538756129d.rlib" "/opt/rustwide/target/debug/deps/libfxhash-4570cd008e269c2c.rlib" "/opt/rustwide/target/debug/deps/libbyteorder-f584045056e081f3.rlib" "/opt/rustwide/target/debug/deps/libpetgraph-3f834334a017f2a6.rlib" "/opt/rustwide/target/debug/deps/libordermap-b73370042704b768.rlib" "/opt/rustwide/target/debug/deps/libfixedbitset-d3fecda4f2080e5e.rlib" "/opt/rustwide/target/debug/deps/libnewtype_derive-9c263ef0a866d441.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-83cafc2ae303332c.rlib" "/opt/rustwide/target/debug/deps/libcustom_derive-d8dafdd0903c1a8d.rlib" "/opt/rustwide/target/debug/deps/libaskama-ffc68cae6d126749.rlib" "/opt/rustwide/target/debug/deps/libaskama_shared-8674891c196cd722.rlib" "/opt/rustwide/target/debug/deps/libhumansize-60a5dd466e1d0b46.rlib" "/opt/rustwide/target/debug/deps/libaskama_escape-6365a6f669fef3d2.rlib" "/opt/rustwide/target/debug/deps/libtoml-f7638888a75f683c.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-1660a65f58d1cb98.rlib" "/opt/rustwide/target/debug/deps/libquick_error-f5a43a4ceb9b7953.rlib" "/opt/rustwide/target/debug/deps/libapprox-e47a466c3ba6501f.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-a4ff9b7e87bbd905.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/libstructopt-e4c16922c8af1941.rlib" "/opt/rustwide/target/debug/deps/libclap-7131737e1990df39.rlib" "/opt/rustwide/target/debug/deps/libyaml_rust-fc9761916af43bee.rlib" "/opt/rustwide/target/debug/deps/libvec_map-9e02dc46b2316171.rlib" "/opt/rustwide/target/debug/deps/libserde-fe43c0c6b938bd64.rlib" "/opt/rustwide/target/debug/deps/libtextwrap-c182af585ce1d152.rlib" "/opt/rustwide/target/debug/deps/libunicode_width-019a22cacfcfb093.rlib" "/opt/rustwide/target/debug/deps/libstrsim-9ecff6948862203f.rlib" "/opt/rustwide/target/debug/deps/libbitflags-4a7b4cf8fbd4dcc3.rlib" "/opt/rustwide/target/debug/deps/libatty-aeb8402cda341d72.rlib" "/opt/rustwide/target/debug/deps/liblibc-a3b13f6b27abcc70.rlib" "/opt/rustwide/target/debug/deps/libansi_term-96d819b388a7bd02.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-aea97a06a6f5704e.rlib(rgsl-aea97a06a6f5704e.rgsl.27vwaqsm-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-aea97a06a6f5704e.rlib(rgsl-aea97a06a6f5704e.rgsl.27vwaqsm-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-aea97a06a6f5704e.rlib(rgsl-aea97a06a6f5704e.rgsl.27vwaqsm-cgu.7.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" "f3c09c29f00219d79dcc94bcd5809b7b6d409e356eafc0d8b89b69fd168a4bc9"` [INFO] running `"docker" "rm" "-f" "f3c09c29f00219d79dcc94bcd5809b7b6d409e356eafc0d8b89b69fd168a4bc9"` [INFO] [stdout] f3c09c29f00219d79dcc94bcd5809b7b6d409e356eafc0d8b89b69fd168a4bc9