[INFO] crate varlociraptor 1.1.1 is already in cache [INFO] extracting crate varlociraptor 1.1.1 into work/ex/beta-1.38-1/sources/1.37.0/reg/varlociraptor/1.1.1 [INFO] extracting crate varlociraptor 1.1.1 into work/ex/beta-1.38-1/sources/beta-2019-08-13/reg/varlociraptor/1.1.1 [INFO] validating manifest of varlociraptor-1.1.1 on toolchain 1.37.0 [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+1.37.0" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] validating manifest of varlociraptor-1.1.1 on toolchain beta-2019-08-13 [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-08-13" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] started frobbing varlociraptor-1.1.1 [INFO] finished frobbing varlociraptor-1.1.1 [INFO] frobbed toml for varlociraptor-1.1.1 written to work/ex/beta-1.38-1/sources/1.37.0/reg/varlociraptor/1.1.1/Cargo.toml [INFO] started frobbing varlociraptor-1.1.1 [INFO] finished frobbing varlociraptor-1.1.1 [INFO] frobbed toml for varlociraptor-1.1.1 written to work/ex/beta-1.38-1/sources/beta-2019-08-13/reg/varlociraptor/1.1.1/Cargo.toml [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+1.37.0" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-08-13" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+1.37.0" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-08-13" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] testing varlociraptor-1.1.1 against beta-2019-08-13 for beta-1.38-1 [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.38-1/worker-0/beta-2019-08-13:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/beta-1.38-1/sources/beta-2019-08-13/reg/varlociraptor/1.1.1:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+beta-2019-08-13" "build" "--frozen"` [INFO] [stdout] 07d5360d824827260a16e0d1a8065d35a6d18f7ff29faa0bf1b8d8f9ff261655 [INFO] running `"docker" "start" "-a" "07d5360d824827260a16e0d1a8065d35a6d18f7ff29faa0bf1b8d8f9ff261655"` [INFO] [stderr] Compiling bindgen v0.51.0 [INFO] [stderr] Compiling ident_case v1.0.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling shlex v0.1.1 [INFO] [stderr] Compiling askama_escape v0.2.0 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling bio v0.28.2 [INFO] [stderr] Compiling derive_builder v0.7.2 [INFO] [stderr] Compiling c_vec v1.0.12 [INFO] [stderr] Compiling strum v0.13.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling custom_error v1.7.1 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling clang-sys v0.28.1 [INFO] [stderr] Compiling fs-utils v1.1.1 [INFO] [stderr] Compiling lzma-sys v0.1.14 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling nom v4.2.3 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling approx v0.3.2 [INFO] [stderr] Compiling counter v0.4.3 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling darling_core v0.9.0 [INFO] [stderr] Compiling pest_generator v2.1.0 [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 ndarray v0.12.1 [INFO] [stderr] Compiling env_logger v0.6.2 [INFO] [stderr] Compiling cexpr v0.3.5 [INFO] [stderr] Compiling vec_map v0.8.1 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling bio-types v0.5.1 [INFO] [stderr] Compiling serde_yaml v0.8.9 [INFO] [stderr] Compiling bio-types v0.4.0 [INFO] [stderr] Compiling pest_derive v2.1.0 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling askama_shared v0.8.0 [INFO] [stderr] Compiling eval v0.4.3 [INFO] [stderr] Compiling clap v2.33.0 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling darling_macro v0.9.0 [INFO] [stderr] Compiling darling v0.9.0 [INFO] [stderr] Compiling askama_derive v0.8.0 [INFO] [stderr] Compiling derive_builder_core v0.5.0 [INFO] [stderr] Compiling structopt v0.2.18 [INFO] [stderr] Compiling askama v0.8.0 [INFO] [stderr] Compiling rust-htslib v0.23.0 [INFO] [stderr] Compiling varlociraptor v1.1.1 (/opt/crater/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/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.0.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.1.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.10.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.11.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.12.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.13.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.14.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.15.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.2.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.3.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.4.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.5.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.6.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.7.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.8.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.varlociraptor.8mkl92xr-cgu.9.rcgu.o" "-o" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122" "/opt/crater/target/debug/deps/varlociraptor-ba7afe9306eb8122.uzupdxsf93q21q0.rcgu.o" "-Wl,--gc-sections" "-pie" "-Wl,-zrelro" "-Wl,-znow" "-nodefaultlibs" "-L" "/opt/crater/target/debug/deps" "-L" "/opt/crater/target/debug/build/rust-htslib-4d264380cc079fae/out" "-L" "/opt/crater/target/debug/build/bzip2-sys-d52c2b633f851508/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/crater/target/debug/deps/libfern-3ab25d39694b4574.rlib" "/opt/crater/target/debug/deps/libvarlociraptor-afcc27603295f035.rlib" "/opt/crater/target/debug/deps/libcounter-cc7a1fc411d31e84.rlib" "/opt/crater/target/debug/deps/libserde_json-5e1c62a001e50ba1.rlib" "/opt/crater/target/debug/deps/libbio_types-97b4050b1e4203db.rlib" "/opt/crater/target/debug/deps/libpest-fe423cd8604aa9c1.rlib" "/opt/crater/target/debug/deps/libucd_trie-8ba25067f5fbb5bb.rlib" "/opt/crater/target/debug/deps/librusty_machine-ca2c1e4185a71ade.rlib" "/opt/crater/target/debug/deps/librulinalg-9eb3aabe48ba51af.rlib" "/opt/crater/target/debug/deps/libnum-a5efe8b19f8dba1e.rlib" "/opt/crater/target/debug/deps/libnum_iter-161e13ffd3321f27.rlib" "/opt/crater/target/debug/deps/libcustom_error-fe269b1b061ee4db.rlib" "/opt/crater/target/debug/deps/libserde_yaml-26dddfb198412fc8.rlib" "/opt/crater/target/debug/deps/libyaml_rust-387383f0fe61ad41.rlib" "/opt/crater/target/debug/deps/liblinked_hash_map-6ecb4766f3b9adc1.rlib" "/opt/crater/target/debug/deps/libdtoa-d00aefffc4eb47c6.rlib" "/opt/crater/target/debug/deps/librgsl-f9c12f99f34319c7.rlib" "/opt/crater/target/debug/deps/libc_vec-0cf308e42bbc7a1f.rlib" "/opt/crater/target/debug/deps/librayon-2ec1357ea6dfa4bb.rlib" "/opt/crater/target/debug/deps/librayon_core-d94e2c45df6d61b3.rlib" "/opt/crater/target/debug/deps/libnum_cpus-b569161181e0c021.rlib" "/opt/crater/target/debug/deps/libcrossbeam_queue-2589c79105784e0d.rlib" "/opt/crater/target/debug/deps/libcrossbeam_deque-3a8837810abbdf66.rlib" "/opt/crater/target/debug/deps/libcrossbeam_epoch-8ce32638c5f827b5.rlib" "/opt/crater/target/debug/deps/libscopeguard-0bc963131f7c0d17.rlib" "/opt/crater/target/debug/deps/libmemoffset-d44318d335d18b97.rlib" "/opt/crater/target/debug/deps/libcrossbeam_utils-e32b73b6a212c837.rlib" "/opt/crater/target/debug/deps/libarrayvec-1cff3f0e2df954b3.rlib" "/opt/crater/target/debug/deps/libnodrop-7f98e5f8ec110eeb.rlib" "/opt/crater/target/debug/deps/librust_htslib-2eaa7f07d26801a3.rlib" "/opt/crater/target/debug/deps/liblzma_sys-9b48331d8968073a.rlib" "/opt/crater/target/debug/deps/libbzip2_sys-be6c2d78c8c718ac.rlib" "/opt/crater/target/debug/deps/liblibz_sys-facd3f421080b4a8.rlib" "/opt/crater/target/debug/deps/liblinear_map-d830d8bc311434c8.rlib" "/opt/crater/target/debug/deps/liburl-ee604ccef16e6499.rlib" "/opt/crater/target/debug/deps/libpercent_encoding-b2b1eddedcc9d5cc.rlib" "/opt/crater/target/debug/deps/libidna-7075ca6261d9bac1.rlib" "/opt/crater/target/debug/deps/libunicode_normalization-b16029f4e9e6461c.rlib" "/opt/crater/target/debug/deps/libsmallvec-7295b1a781bd56b7.rlib" "/opt/crater/target/debug/deps/libunicode_bidi-020a270ca49d2bee.rlib" "/opt/crater/target/debug/deps/libmatches-9f7ad04d44b47530.rlib" "/opt/crater/target/debug/deps/libieee754-47d71936b5606ce4.rlib" "/opt/crater/target/debug/deps/libbitflags-87aacccedafc3e9f.rlib" "/opt/crater/target/debug/deps/libitertools-7a59558413d02103.rlib" "/opt/crater/target/debug/deps/libbio-373069d9f64d43d3.rlib" "/opt/crater/target/debug/deps/libstrum-7d39a279786b0755.rlib" "/opt/crater/target/debug/deps/libitertools_num-563bb5ab93ae8895.rlib" "/opt/crater/target/debug/deps/libstatrs-1e87fbef523ea00f.rlib" "/opt/crater/target/debug/deps/librand-5eda43279f0ef45c.rlib" "/opt/crater/target/debug/deps/librand-7efbcbd89944bda6.rlib" "/opt/crater/target/debug/deps/libordered_float-4ac8fd4105c2b159.rlib" "/opt/crater/target/debug/deps/libndarray-00b34b01b5e032d5.rlib" "/opt/crater/target/debug/deps/libnum_complex-2fa6bf14402c9fb0.rlib" "/opt/crater/target/debug/deps/libmatrixmultiply-b856c59a72f2ed38.rlib" "/opt/crater/target/debug/deps/librawpointer-65262f271f4611c8.rlib" "/opt/crater/target/debug/deps/libmultimap-e67ae403e52c5a00.rlib" "/opt/crater/target/debug/deps/libitertools-42e27b01991a8665.rlib" "/opt/crater/target/debug/deps/libeither-0991b1b51775eba9.rlib" "/opt/crater/target/debug/deps/libcsv-0e48c8e58ebc3176.rlib" "/opt/crater/target/debug/deps/libryu-a9583eff3872e809.rlib" "/opt/crater/target/debug/deps/libitoa-fbd08118d5c2ed14.rlib" "/opt/crater/target/debug/deps/libcsv_core-1781c259496f45f1.rlib" "/opt/crater/target/debug/deps/libbstr-b9fd8370179b3b1d.rlib" "/opt/crater/target/debug/deps/libregex_automata-a07793a8fb895fbe.rlib" "/opt/crater/target/debug/deps/libnum_integer-440f23443e3e87b1.rlib" "/opt/crater/target/debug/deps/libbv-e349db919246f342.rlib" "/opt/crater/target/debug/deps/libbytecount-3305905a12bdf926.rlib" "/opt/crater/target/debug/deps/libbit_set-089248f87181368e.rlib" "/opt/crater/target/debug/deps/libbit_vec-89b806e996bd3ca1.rlib" "/opt/crater/target/debug/deps/libbio_types-9ddcb76b4dea3c40.rlib" "/opt/crater/target/debug/deps/libregex-66a568a007ba35d5.rlib" "/opt/crater/target/debug/deps/libregex_syntax-bd99c61924ee7656.rlib" "/opt/crater/target/debug/deps/libthread_local-2ae771cec36f83c2.rlib" "/opt/crater/target/debug/deps/libaho_corasick-83b7acf69cd770dd.rlib" "/opt/crater/target/debug/deps/libmemchr-8599562422b87512.rlib" "/opt/crater/target/debug/deps/libfxhash-4124a3dcd49470d3.rlib" "/opt/crater/target/debug/deps/libbyteorder-98f71e4258b709b0.rlib" "/opt/crater/target/debug/deps/libpetgraph-0342de6fc4669b92.rlib" "/opt/crater/target/debug/deps/libordermap-d1c8c912bd325bdf.rlib" "/opt/crater/target/debug/deps/libfixedbitset-c4b66e82eedacb07.rlib" "/opt/crater/target/debug/deps/libnewtype_derive-50f86e94e5894903.rlib" "/opt/crater/target/debug/deps/liblazy_static-1f7a4359e40a6da9.rlib" "/opt/crater/target/debug/deps/libcustom_derive-0f45cb4ce8c03868.rlib" "/opt/crater/target/debug/deps/libaskama-663ed7a199cdb0df.rlib" "/opt/crater/target/debug/deps/libaskama_shared-ac193dc3f0116ff9.rlib" "/opt/crater/target/debug/deps/libhumansize-b205f407b7f0b32b.rlib" "/opt/crater/target/debug/deps/libaskama_escape-c57d24456b786d04.rlib" "/opt/crater/target/debug/deps/libtoml-a66c94a4c31323f1.rlib" "/opt/crater/target/debug/deps/liblazy_static-8e8f275d3efea5b8.rlib" "/opt/crater/target/debug/deps/libquick_error-f50ea951eae373ef.rlib" "/opt/crater/target/debug/deps/libapprox-6a6bdd1ea8ffac53.rlib" "/opt/crater/target/debug/deps/libnum_traits-c28daeab5210b49d.rlib" "/opt/crater/target/debug/deps/liblog-c97b73a8bcee9985.rlib" "/opt/crater/target/debug/deps/liblog-6796845c78a3960b.rlib" "/opt/crater/target/debug/deps/libcfg_if-c978b2f886ff1de7.rlib" "/opt/crater/target/debug/deps/libstructopt-f0cddc205033430c.rlib" "/opt/crater/target/debug/deps/libclap-f0d9999040fbebcd.rlib" "/opt/crater/target/debug/deps/libyaml_rust-7f90bfa09845735f.rlib" "/opt/crater/target/debug/deps/libvec_map-149d3001e0b60fe7.rlib" "/opt/crater/target/debug/deps/libserde-50e5d46514dccf4f.rlib" "/opt/crater/target/debug/deps/libtextwrap-648e6ff45e87fdf7.rlib" "/opt/crater/target/debug/deps/libunicode_width-c482f247a0e67224.rlib" "/opt/crater/target/debug/deps/libstrsim-71052c127de7173f.rlib" "/opt/crater/target/debug/deps/libbitflags-c2b055ef483e7b37.rlib" "/opt/crater/target/debug/deps/libatty-22eb3b2ac1d714c2.rlib" "/opt/crater/target/debug/deps/liblibc-37f3d1c853b3b7bd.rlib" "/opt/crater/target/debug/deps/libansi_term-8091014737d4fb0a.rlib" "-Wl,--start-group" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-1d6d86bd078a28e9.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-e9721e46a424e2a9.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace-c07193698f282147.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace_sys-6da45690f3863086.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-690797036dd27680.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-d3896ccbfd8eda2b.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-7cccc3739e3d7623.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-5e9ba178a513cd29.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-5ca9f83bf63d1f4b.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-bba1c7ef9e950882.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-e23c9de62012deb5.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-9b59dffdcd513d5d.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-17392340ab2e4a97.rlib" "-Wl,--end-group" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-ac21508a81e3f7f3.rlib" "-Wl,-Bdynamic" "-llzma" "-lz" "-lutil" "-lutil" "-ldl" "-lrt" "-lpthread" "-lgcc_s" "-lc" "-lm" "-lrt" "-lpthread" "-lutil" "-lutil" [INFO] [stderr] = note: /opt/crater/target/debug/deps/librgsl-f9c12f99f34319c7.rlib(rgsl-f9c12f99f34319c7.rgsl.cttudxnm-cgu.13.rcgu.o): In function `rgsl::randist::gaussian::ugaussian_P': [INFO] [stderr] /opt/crater/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/crater/target/debug/deps/librgsl-f9c12f99f34319c7.rlib(rgsl-f9c12f99f34319c7.rgsl.cttudxnm-cgu.14.rcgu.o): In function `rgsl::randist::binomial::binomial_pdf': [INFO] [stderr] /opt/crater/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/crater/target/debug/deps/librgsl-f9c12f99f34319c7.rlib(rgsl-f9c12f99f34319c7.rgsl.cttudxnm-cgu.7.rcgu.o): In function `rgsl::randist::poisson::poisson_pdf': [INFO] [stderr] /opt/crater/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" "07d5360d824827260a16e0d1a8065d35a6d18f7ff29faa0bf1b8d8f9ff261655"` [INFO] running `"docker" "rm" "-f" "07d5360d824827260a16e0d1a8065d35a6d18f7ff29faa0bf1b8d8f9ff261655"` [INFO] [stdout] 07d5360d824827260a16e0d1a8065d35a6d18f7ff29faa0bf1b8d8f9ff261655