[INFO] fetching crate varlociraptor 1.1.1... [INFO] extracting crate varlociraptor 1.1.1 into work/ex/beta-1.37-6/sources/1.36.0/reg/varlociraptor/1.1.1 [INFO] extracting crate varlociraptor 1.1.1 into work/ex/beta-1.37-6/sources/beta-2019-07-23/reg/varlociraptor/1.1.1 [INFO] validating manifest of varlociraptor-1.1.1 on toolchain 1.36.0 [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+1.36.0" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] validating manifest of varlociraptor-1.1.1 on toolchain beta-2019-07-23 [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-07-23" "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-1.37-6/sources/1.36.0/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-1.37-6/sources/beta-2019-07-23/reg/varlociraptor/1.1.1/Cargo.toml [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+1.36.0" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-07-23" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+1.36.0" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+beta-2019-07-23" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] testing varlociraptor-1.1.1 against beta-2019-07-23 for beta-1.37-6 [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.37-6/worker-7/beta-2019-07-23:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/beta-1.37-6/sources/beta-2019-07-23/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-2019-07-23" "build" "--frozen"` [INFO] [stdout] 16d1c4db25f32222e9afaed1ea861e9f533da2528c664b4b86665c004466b30d [INFO] running `"docker" "start" "-a" "16d1c4db25f32222e9afaed1ea861e9f533da2528c664b4b86665c004466b30d"` [INFO] [stderr] Compiling bindgen v0.51.0 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling ucd-trie v0.1.2 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling askama_escape v0.2.0 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling derive_builder v0.7.2 [INFO] [stderr] Compiling bio v0.28.2 [INFO] [stderr] Compiling strum v0.13.0 [INFO] [stderr] Compiling custom_error v1.7.1 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling num-complex v0.2.3 [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 pest v2.1.1 [INFO] [stderr] Compiling nom v4.2.3 [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 darling_core v0.9.0 [INFO] [stderr] Compiling structopt-derive v0.2.18 [INFO] [stderr] Compiling strum_macros v0.13.0 [INFO] [stderr] Compiling derive-new v0.5.7 [INFO] [stderr] Compiling getset v0.0.7 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling serde v1.0.98 [INFO] [stderr] Compiling pest_meta v2.1.1 [INFO] [stderr] Compiling cexpr v0.3.5 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling darling_macro v0.9.0 [INFO] [stderr] Compiling pest_generator v2.1.0 [INFO] [stderr] Compiling darling v0.9.0 [INFO] [stderr] Compiling derive_builder_core v0.5.0 [INFO] [stderr] Compiling pest_derive v2.1.0 [INFO] [stderr] Compiling vec_map v0.8.1 [INFO] [stderr] Compiling toml v0.4.10 [INFO] [stderr] Compiling bstr v0.2.6 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling serde_json v1.0.40 [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 clap v2.33.0 [INFO] [stderr] Compiling csv v1.1.1 [INFO] [stderr] Compiling eval v0.4.3 [INFO] [stderr] Compiling askama_shared v0.8.0 [INFO] [stderr] Compiling askama_derive v0.8.0 [INFO] [stderr] Compiling askama v0.8.0 [INFO] [stderr] Compiling structopt v0.2.18 [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] 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-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.0.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.1.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.10.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.11.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.12.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.13.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.14.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.15.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.2.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.3.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.4.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.5.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.6.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.7.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.8.rcgu.o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.varlociraptor.bj2dj7g9-cgu.9.rcgu.o" "-o" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39" "/opt/crater/target/debug/deps/varlociraptor-c2ce3777f4b50b39.4q779yre39h83bgb.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-0630d20c11d0fed8/out" "-L" "/opt/crater/target/debug/build/bzip2-sys-5ffaf2b43e086c26/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/crater/target/debug/deps/libfern-ac3ceed81fe12464.rlib" "/opt/crater/target/debug/deps/libvarlociraptor-3abfe710559eefa7.rlib" "/opt/crater/target/debug/deps/libcounter-8ab75ad849b8cb49.rlib" "/opt/crater/target/debug/deps/libserde_json-0928c2c1a73931e7.rlib" "/opt/crater/target/debug/deps/libbio_types-243b409ac9991fe9.rlib" "/opt/crater/target/debug/deps/libpest-32d2d90543fed1e8.rlib" "/opt/crater/target/debug/deps/libucd_trie-b27403803b8610bd.rlib" "/opt/crater/target/debug/deps/librusty_machine-d9ab6883a7d38e07.rlib" "/opt/crater/target/debug/deps/librulinalg-c0bd0f306776bf8f.rlib" "/opt/crater/target/debug/deps/libnum-afef0f025f3e4a93.rlib" "/opt/crater/target/debug/deps/libnum_iter-6aa8c2e263944e3d.rlib" "/opt/crater/target/debug/deps/libcustom_error-3ac7fdfa0d56204f.rlib" "/opt/crater/target/debug/deps/libserde_yaml-44f5b4db8667b199.rlib" "/opt/crater/target/debug/deps/libyaml_rust-b0de4a487f0df794.rlib" "/opt/crater/target/debug/deps/liblinked_hash_map-64b5808476af51a2.rlib" "/opt/crater/target/debug/deps/libdtoa-d816c76c22d8db3a.rlib" "/opt/crater/target/debug/deps/librgsl-73d61827b825a3ff.rlib" "/opt/crater/target/debug/deps/libc_vec-0c288992332fe7e9.rlib" "/opt/crater/target/debug/deps/librayon-0085977b8f7ca5e8.rlib" "/opt/crater/target/debug/deps/librayon_core-79d59f67ce9478e1.rlib" "/opt/crater/target/debug/deps/libnum_cpus-2c854131c0da7b53.rlib" "/opt/crater/target/debug/deps/libcrossbeam_queue-9a19686c8121c25b.rlib" "/opt/crater/target/debug/deps/libcrossbeam_deque-443dfff47063a34e.rlib" "/opt/crater/target/debug/deps/libcrossbeam_epoch-64e8ef56c5fe0efe.rlib" "/opt/crater/target/debug/deps/libscopeguard-690e8e7efd40245c.rlib" "/opt/crater/target/debug/deps/libmemoffset-4e66c457697043a8.rlib" "/opt/crater/target/debug/deps/libcrossbeam_utils-41fe25ba70f5455e.rlib" "/opt/crater/target/debug/deps/libarrayvec-1041925da7343e83.rlib" "/opt/crater/target/debug/deps/libnodrop-36ce0cdfb7359e6a.rlib" "/opt/crater/target/debug/deps/librust_htslib-a759642fa3711be8.rlib" "/opt/crater/target/debug/deps/liblzma_sys-eed3c4f66122e468.rlib" "/opt/crater/target/debug/deps/libbzip2_sys-49ee1ec4d00c3f8f.rlib" "/opt/crater/target/debug/deps/liblibz_sys-a007439c1d8c8af0.rlib" "/opt/crater/target/debug/deps/liblinear_map-edcbae2908f2f4a8.rlib" "/opt/crater/target/debug/deps/liburl-4858f7c80a0a9641.rlib" "/opt/crater/target/debug/deps/libpercent_encoding-880723daba293888.rlib" "/opt/crater/target/debug/deps/libidna-f1bd554acf3de410.rlib" "/opt/crater/target/debug/deps/libunicode_normalization-b016911b6ed6746c.rlib" "/opt/crater/target/debug/deps/libsmallvec-3009c93eda7cf4fa.rlib" "/opt/crater/target/debug/deps/libunicode_bidi-c4ef84e7768feceb.rlib" "/opt/crater/target/debug/deps/libmatches-4743b9188552617d.rlib" "/opt/crater/target/debug/deps/libieee754-3e184d4e293fe88a.rlib" "/opt/crater/target/debug/deps/libbitflags-3e0496368fb8d844.rlib" "/opt/crater/target/debug/deps/libitertools-0f3b2e1a480bd495.rlib" "/opt/crater/target/debug/deps/libbio-f5579953e11416e7.rlib" "/opt/crater/target/debug/deps/libstrum-dbba4a2a853f2c4b.rlib" "/opt/crater/target/debug/deps/libitertools_num-0beab66c935d40ce.rlib" "/opt/crater/target/debug/deps/libstatrs-27ab7b4b694d286b.rlib" "/opt/crater/target/debug/deps/librand-e08ba8aab010d886.rlib" "/opt/crater/target/debug/deps/librand-12c0152561214ea4.rlib" "/opt/crater/target/debug/deps/libordered_float-9f47dd5d16d4d052.rlib" "/opt/crater/target/debug/deps/libndarray-ff66d75febced50c.rlib" "/opt/crater/target/debug/deps/libnum_complex-cf92338cbd917405.rlib" "/opt/crater/target/debug/deps/libmatrixmultiply-add3c2ef4a6aa2e3.rlib" "/opt/crater/target/debug/deps/librawpointer-0c16108fbcdeefb9.rlib" "/opt/crater/target/debug/deps/libmultimap-acc897204f785bfc.rlib" "/opt/crater/target/debug/deps/libitertools-ec3709ec2ec15838.rlib" "/opt/crater/target/debug/deps/libeither-09ec7c1188b8d0d0.rlib" "/opt/crater/target/debug/deps/libcsv-b1fb023cfaf62f06.rlib" "/opt/crater/target/debug/deps/libryu-2328132eba3746b3.rlib" "/opt/crater/target/debug/deps/libitoa-97a946ec35c116e9.rlib" "/opt/crater/target/debug/deps/libcsv_core-73dfa375e200bd62.rlib" "/opt/crater/target/debug/deps/libbstr-8727d84f572d01a0.rlib" "/opt/crater/target/debug/deps/libregex_automata-5cec955928a143a3.rlib" "/opt/crater/target/debug/deps/libnum_integer-35be16e7600d6cb9.rlib" "/opt/crater/target/debug/deps/libbv-e06ad3f5c7359448.rlib" "/opt/crater/target/debug/deps/libbytecount-42e9d9beb000108d.rlib" "/opt/crater/target/debug/deps/libbit_set-469736b20aa8bbf5.rlib" "/opt/crater/target/debug/deps/libbit_vec-fa07c09034eb3f1d.rlib" "/opt/crater/target/debug/deps/libbio_types-5ff79a8a306fd848.rlib" "/opt/crater/target/debug/deps/libregex-d1e674bef6ddd023.rlib" "/opt/crater/target/debug/deps/libutf8_ranges-32fecc95d998aacd.rlib" "/opt/crater/target/debug/deps/libregex_syntax-df3af46a51d0ff63.rlib" "/opt/crater/target/debug/deps/libucd_util-3795c9684c4c7e7c.rlib" "/opt/crater/target/debug/deps/libthread_local-1060038c0757fbc7.rlib" "/opt/crater/target/debug/deps/libaho_corasick-9b9fe170847273a7.rlib" "/opt/crater/target/debug/deps/libmemchr-f949e5689323dbe6.rlib" "/opt/crater/target/debug/deps/libfxhash-fa9b3e4513ced53a.rlib" "/opt/crater/target/debug/deps/libbyteorder-066131f17ea0c99b.rlib" "/opt/crater/target/debug/deps/libpetgraph-b3fe8005560a6084.rlib" "/opt/crater/target/debug/deps/libordermap-27eb3e7e20fdaed2.rlib" "/opt/crater/target/debug/deps/libfixedbitset-6340672f15b02884.rlib" "/opt/crater/target/debug/deps/libnewtype_derive-bce3ef0b423c857d.rlib" "/opt/crater/target/debug/deps/liblazy_static-6a4e8ea56a445919.rlib" "/opt/crater/target/debug/deps/libcustom_derive-c1793975d6464a26.rlib" "/opt/crater/target/debug/deps/libaskama-50f53d02635a9f91.rlib" "/opt/crater/target/debug/deps/libaskama_shared-be35521e20f346fd.rlib" "/opt/crater/target/debug/deps/libhumansize-e802c0fae73f1b44.rlib" "/opt/crater/target/debug/deps/libaskama_escape-e5405246e19b3b0f.rlib" "/opt/crater/target/debug/deps/libtoml-b0b8f40e2da6e627.rlib" "/opt/crater/target/debug/deps/liblazy_static-0e1e36676eed3924.rlib" "/opt/crater/target/debug/deps/libquick_error-7d23d7c8e4749989.rlib" "/opt/crater/target/debug/deps/libapprox-0be3ec18c32ebe3c.rlib" "/opt/crater/target/debug/deps/libnum_traits-04277105b9bd2221.rlib" "/opt/crater/target/debug/deps/liblog-bbe9110cf0409309.rlib" "/opt/crater/target/debug/deps/liblog-4d4ce27474bb9998.rlib" "/opt/crater/target/debug/deps/libcfg_if-17244d8fcea476bd.rlib" "/opt/crater/target/debug/deps/libstructopt-d95af4655f7b6b7a.rlib" "/opt/crater/target/debug/deps/libclap-92561e44bb79c27c.rlib" "/opt/crater/target/debug/deps/libyaml_rust-e06fbadedaa4d350.rlib" "/opt/crater/target/debug/deps/libvec_map-511d5aaaa61250f8.rlib" "/opt/crater/target/debug/deps/libserde-c0ce82fcdba3ba6f.rlib" "/opt/crater/target/debug/deps/libtextwrap-a7f85f046874f4da.rlib" "/opt/crater/target/debug/deps/libunicode_width-5c65625ac38072b6.rlib" "/opt/crater/target/debug/deps/libstrsim-b714068d90a275c7.rlib" "/opt/crater/target/debug/deps/libbitflags-1f73faaef27177be.rlib" "/opt/crater/target/debug/deps/libatty-03bfb70b48d44ab1.rlib" "/opt/crater/target/debug/deps/liblibc-15b143653abd1ffe.rlib" "/opt/crater/target/debug/deps/libansi_term-a8ee7a34610f25b5.rlib" "-Wl,--start-group" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-a80a1e8e09cafef8.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-e0e6351da805c468.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace-e04f54bafc95e331.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace_sys-67901d3322495bd5.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-bd390b1abaceaec1.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-312dd37fdc7bedfc.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-8ed0e51d58d644a3.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-8a423c320a6c707f.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-d6a95598e2238263.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-d231614b153016eb.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-3821619027f463e4.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-1cfd794d18771a44.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-dcf33cf10c2452ef.rlib" "-Wl,--end-group" "/opt/crater/rustup-home/toolchains/beta-2019-07-23-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-c258fea34bf64bce.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-73d61827b825a3ff.rlib(rgsl-73d61827b825a3ff.rgsl.rv9j12ro-cgu.11.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-73d61827b825a3ff.rlib(rgsl-73d61827b825a3ff.rgsl.rv9j12ro-cgu.13.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-73d61827b825a3ff.rlib(rgsl-73d61827b825a3ff.rgsl.rv9j12ro-cgu.6.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" "16d1c4db25f32222e9afaed1ea861e9f533da2528c664b4b86665c004466b30d"` [INFO] running `"docker" "rm" "-f" "16d1c4db25f32222e9afaed1ea861e9f533da2528c664b4b86665c004466b30d"` [INFO] [stdout] 16d1c4db25f32222e9afaed1ea861e9f533da2528c664b4b86665c004466b30d