[INFO] crate libprosic 0.7.3 is already in cache [INFO] extracting crate libprosic 0.7.3 into work/ex/beta-1.38-1/sources/1.37.0/reg/libprosic/0.7.3 [INFO] extracting crate libprosic 0.7.3 into work/ex/beta-1.38-1/sources/beta-2019-08-13/reg/libprosic/0.7.3 [INFO] validating manifest of libprosic-0.7.3 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 libprosic-0.7.3 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 libprosic-0.7.3 [INFO] finished frobbing libprosic-0.7.3 [INFO] frobbed toml for libprosic-0.7.3 written to work/ex/beta-1.38-1/sources/1.37.0/reg/libprosic/0.7.3/Cargo.toml [INFO] started frobbing libprosic-0.7.3 [INFO] finished frobbing libprosic-0.7.3 [INFO] frobbed toml for libprosic-0.7.3 written to work/ex/beta-1.38-1/sources/beta-2019-08-13/reg/libprosic/0.7.3/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 libprosic-0.7.3 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-2/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/libprosic/0.7.3:/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] c5b9928632438d2e78b7d35d2959997b4902658ef07d1123fbeb01876477061c [INFO] running `"docker" "start" "-a" "c5b9928632438d2e78b7d35d2959997b4902658ef07d1123fbeb01876477061c"` [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling memchr v2.2.1 [INFO] [stderr] Compiling bzip2-sys v0.1.7 [INFO] [stderr] Compiling lzma-sys v0.1.15 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Compiling statrs v0.9.0 [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 aho-corasick v0.6.10 [INFO] [stderr] Compiling bstr v0.2.7 [INFO] [stderr] Compiling csv-core v0.1.6 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling regex v1.2.1 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling csv v1.1.1 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Compiling bio-types v0.5.1 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/crater/workdir) [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call/pairwise.rs:55:62 [INFO] [stderr] | [INFO] [stderr] 55 | ) -> Result>>, Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(bare_trait_objects)]` on by default [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call/pairwise.rs:116:21 [INFO] [stderr] | [INFO] [stderr] 116 | ) -> Result<(), Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/alignment_properties.rs:40:68 [INFO] [stderr] | [INFO] [stderr] 40 | pub fn estimate(bam: &mut R) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/alignment_properties.rs:142:33 [INFO] [stderr] | [INFO] [stderr] 142 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/fdr/ev.rs:35:21 [INFO] [stderr] | [INFO] [stderr] 35 | ) -> Result<(), Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:52:89 [INFO] [stderr] | [INFO] [stderr] 52 | pub fn estimate_insert_size(left: &bam::Record, right: &bam::Record) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:56:68 [INFO] [stderr] | [INFO] [stderr] 56 | let aln = |rec: &bam::Record, cigar| -> Result<(u32, u32), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:120:41 [INFO] [stderr] | [INFO] [stderr] 120 | ) -> Result<(LogProb, LogProb), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:30:49 [INFO] [stderr] | [INFO] [stderr] 30 | ) -> Result, Box>; [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:56:49 [INFO] [stderr] | [INFO] [stderr] 56 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:101:49 [INFO] [stderr] | [INFO] [stderr] 101 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:169:49 [INFO] [stderr] | [INFO] [stderr] 169 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:68:82 [INFO] [stderr] | [INFO] [stderr] 68 | pub fn fill(&mut self, chrom: &[u8], start: u32, end: u32) -> Result<(), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:220:39 [INFO] [stderr] | [INFO] [stderr] 220 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:362:42 [INFO] [stderr] | [INFO] [stderr] 362 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:363:34 [INFO] [stderr] | [INFO] [stderr] 363 | let mut evidence: RefMut = match variant { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn evidence::reads::AbstractReadEvidence` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:409:42 [INFO] [stderr] | [INFO] [stderr] 409 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:412:44 [INFO] [stderr] | [INFO] [stderr] 412 | -> Result<(LogProb, LogProb), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/mod.rs:275:41 [INFO] [stderr] | [INFO] [stderr] 275 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/mod.rs:416:42 [INFO] [stderr] | [INFO] [stderr] 416 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:27:46 [INFO] [stderr] | [INFO] [stderr] 27 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:204:62 [INFO] [stderr] | [INFO] [stderr] 204 | pub fn seq(&mut self, chrom: &[u8]) -> Result<&[u8], Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:232:39 [INFO] [stderr] | [INFO] [stderr] 232 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:276:35 [INFO] [stderr] | [INFO] [stderr] 276 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:317:21 [INFO] [stderr] | [INFO] [stderr] 317 | ) -> Result<(), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:367:30 [INFO] [stderr] | [INFO] [stderr] 367 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'std::sync::ONCE_INIT': the `new` function is now preferred [INFO] [stderr] --> src/model/evidence/reads.rs:335:1 [INFO] [stderr] | [INFO] [stderr] 335 | / lazy_static! { [INFO] [stderr] 336 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stderr] 337 | | } [INFO] [stderr] | |_^ [INFO] [stderr] | [INFO] [stderr] = note: `#[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/priors/single_cell_bulk.rs:26:1 [INFO] [stderr] | [INFO] [stderr] 26 | / cached! { [INFO] [stderr] 27 | | AMPLIF_CACHE: UnboundCache<(AlleleFreq, usize, usize), LogProb> = UnboundCache::new(); [INFO] [stderr] 28 | | // Lodato et al. 2015, Science, Supplementary Information, pages 8f and Fig. S5 (A, C, E) [INFO] [stderr] 29 | | // TODO: allow for non-default Lodato model parameters, e.g. learned from the data at hand [INFO] [stderr] ... | [INFO] [stderr] 96 | | } [INFO] [stderr] 97 | | } [INFO] [stderr] | |_^ [INFO] [stderr] | [INFO] [stderr] = note: this warning originates in a macro outside of the current crate (in Nightly builds, run with -Z external-macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 25s [INFO] running `"docker" "inspect" "c5b9928632438d2e78b7d35d2959997b4902658ef07d1123fbeb01876477061c"` [INFO] running `"docker" "rm" "-f" "c5b9928632438d2e78b7d35d2959997b4902658ef07d1123fbeb01876477061c"` [INFO] [stdout] c5b9928632438d2e78b7d35d2959997b4902658ef07d1123fbeb01876477061c [INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/beta-1.38-1/worker-2/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/libprosic/0.7.3:/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" "test" "--frozen" "--no-run"` [INFO] [stdout] 77a30e3976dc21089c3b4e04fc89cac802e3ba557f4df88ae1ba1648d2551a52 [INFO] running `"docker" "start" "-a" "77a30e3976dc21089c3b4e04fc89cac802e3ba557f4df88ae1ba1648d2551a52"` [INFO] [stderr] Compiling memchr v0.1.11 [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling thread-id v2.0.0 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] Compiling thread_local v0.2.7 [INFO] [stderr] Compiling flate2 v0.2.20 [INFO] [stderr] Compiling aho-corasick v0.5.3 [INFO] [stderr] Compiling regex v0.1.80 [INFO] [stderr] Compiling env_logger v0.3.5 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/crater/workdir) [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call/pairwise.rs:55:62 [INFO] [stderr] | [INFO] [stderr] 55 | ) -> Result>>, Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(bare_trait_objects)]` on by default [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/call/pairwise.rs:116:21 [INFO] [stderr] | [INFO] [stderr] 116 | ) -> Result<(), Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/alignment_properties.rs:40:68 [INFO] [stderr] | [INFO] [stderr] 40 | pub fn estimate(bam: &mut R) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/alignment_properties.rs:142:33 [INFO] [stderr] | [INFO] [stderr] 142 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/estimation/fdr/ev.rs:35:21 [INFO] [stderr] | [INFO] [stderr] 35 | ) -> Result<(), Box> [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:52:89 [INFO] [stderr] | [INFO] [stderr] 52 | pub fn estimate_insert_size(left: &bam::Record, right: &bam::Record) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:56:68 [INFO] [stderr] | [INFO] [stderr] 56 | let aln = |rec: &bam::Record, cigar| -> Result<(u32, u32), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/fragments.rs:120:41 [INFO] [stderr] | [INFO] [stderr] 120 | ) -> Result<(LogProb, LogProb), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:30:49 [INFO] [stderr] | [INFO] [stderr] 30 | ) -> Result, Box>; [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:56:49 [INFO] [stderr] | [INFO] [stderr] 56 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:101:49 [INFO] [stderr] | [INFO] [stderr] 101 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/evidence/reads.rs:169:49 [INFO] [stderr] | [INFO] [stderr] 169 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:68:82 [INFO] [stderr] | [INFO] [stderr] 68 | pub fn fill(&mut self, chrom: &[u8], start: u32, end: u32) -> Result<(), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:220:39 [INFO] [stderr] | [INFO] [stderr] 220 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:362:42 [INFO] [stderr] | [INFO] [stderr] 362 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:363:34 [INFO] [stderr] | [INFO] [stderr] 363 | let mut evidence: RefMut = match variant { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `dyn evidence::reads::AbstractReadEvidence` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:409:42 [INFO] [stderr] | [INFO] [stderr] 409 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/sample.rs:412:44 [INFO] [stderr] | [INFO] [stderr] 412 | -> Result<(LogProb, LogProb), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/mod.rs:275:41 [INFO] [stderr] | [INFO] [stderr] 275 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/model/mod.rs:416:42 [INFO] [stderr] | [INFO] [stderr] 416 | ) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:27:46 [INFO] [stderr] | [INFO] [stderr] 27 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:204:62 [INFO] [stderr] | [INFO] [stderr] 204 | pub fn seq(&mut self, chrom: &[u8]) -> Result<&[u8], Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:232:39 [INFO] [stderr] | [INFO] [stderr] 232 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:276:35 [INFO] [stderr] | [INFO] [stderr] 276 | ) -> Result>, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:317:21 [INFO] [stderr] | [INFO] [stderr] 317 | ) -> Result<(), Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:367:30 [INFO] [stderr] | [INFO] [stderr] 367 | ) -> Result> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'std::sync::ONCE_INIT': the `new` function is now preferred [INFO] [stderr] --> src/model/evidence/reads.rs:335:1 [INFO] [stderr] | [INFO] [stderr] 335 | / lazy_static! { [INFO] [stderr] 336 | | static ref PROB_CONFUSION: LogProb = LogProb::from(Prob(0.3333)); [INFO] [stderr] 337 | | } [INFO] [stderr] | |_^ [INFO] [stderr] | [INFO] [stderr] = note: `#[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/priors/single_cell_bulk.rs:26:1 [INFO] [stderr] | [INFO] [stderr] 26 | / cached! { [INFO] [stderr] 27 | | AMPLIF_CACHE: UnboundCache<(AlleleFreq, usize, usize), LogProb> = UnboundCache::new(); [INFO] [stderr] 28 | | // Lodato et al. 2015, Science, Supplementary Information, pages 8f and Fig. S5 (A, C, E) [INFO] [stderr] 29 | | // TODO: allow for non-default Lodato model parameters, e.g. learned from the data at hand [INFO] [stderr] ... | [INFO] [stderr] 96 | | } [INFO] [stderr] 97 | | } [INFO] [stderr] | |_^ [INFO] [stderr] | [INFO] [stderr] = note: this warning originates in a macro 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/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.0.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.1.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.10.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.11.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.12.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.13.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.14.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.15.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.2.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.3.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.4.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.5.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.6.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.7.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.8.rcgu.o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.libprosic.62cza2n8-cgu.9.rcgu.o" "-o" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df" "/opt/crater/target/debug/deps/libprosic-5b7773f07298a3df.hk2ny5659jcrmd0.rcgu.o" "-Wl,--gc-sections" "-pie" "-Wl,-zrelro" "-Wl,-znow" "-nodefaultlibs" "-L" "/opt/crater/target/debug/deps" "-L" "/opt/crater/target/debug/build/miniz-sys-e6b91e84307dae80/out" "-L" "/opt/crater/target/debug/build/rust-htslib-1309cfcd697f0833/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/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libtest-f0d86b2ef6410e4f.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libterm-28a84d78fba0104f.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgetopts-625008d0a6744ece.rlib" "/opt/crater/rustup-home/toolchains/beta-2019-08-13-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunicode_width-b85c11af396739da.rlib" "/opt/crater/target/debug/deps/libenv_logger-de72903a2cda97ec.rlib" "/opt/crater/target/debug/deps/libregex-7aad24a91d67a202.rlib" "/opt/crater/target/debug/deps/libutf8_ranges-f03f24c2204694fb.rlib" "/opt/crater/target/debug/deps/libregex_syntax-e4e7cc24efed9736.rlib" "/opt/crater/target/debug/deps/libthread_local-c9ae6212acc6f742.rlib" "/opt/crater/target/debug/deps/libthread_id-52668e43ea947c6f.rlib" "/opt/crater/target/debug/deps/libaho_corasick-840ce1fc56dd2971.rlib" "/opt/crater/target/debug/deps/libmemchr-680712307a1b2418.rlib" "/opt/crater/target/debug/deps/libcached-87e42617795611f3.rlib" "/opt/crater/target/debug/deps/libregex-da9a5ed411f64e31.rlib" "/opt/crater/target/debug/deps/libutf8_ranges-cc1cabb2cf7145bf.rlib" "/opt/crater/target/debug/deps/libregex_syntax-f02878b30c9311c4.rlib" "/opt/crater/target/debug/deps/libucd_util-c0b3d8114e0f53f5.rlib" "/opt/crater/target/debug/deps/libaho_corasick-0aae1a61ace9f262.rlib" "/opt/crater/target/debug/deps/librusty_machine-25895eb7c26707f4.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/libndarray-bc21feda0e93988b.rlib" "/opt/crater/target/debug/deps/libnum_complex-7b0b3f6936f1678f.rlib" "/opt/crater/target/debug/deps/libnum_traits-85d0e05aa2cc3298.rlib" "/opt/crater/target/debug/deps/libitertools-52dfee8dc6355025.rlib" "/opt/crater/target/debug/deps/libapprox-979a4cb7f16d22ee.rlib" "/opt/crater/target/debug/deps/librgsl-ef2a4b8ea9f786e7.rlib" "/opt/crater/target/debug/deps/libc_vec-0cf308e42bbc7a1f.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/librust_htslib-aaf8e5dc7ad19747.rlib" "/opt/crater/target/debug/deps/liblzma_sys-ca1219f7f754b5f3.rlib" "/opt/crater/target/debug/deps/libbzip2_sys-9d85b288a7d1a64a.rlib" "/opt/crater/target/debug/deps/liblibz_sys-4aad2fd800a79889.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/liblazy_static-8e8f275d3efea5b8.rlib" "/opt/crater/target/debug/deps/libitertools-49d310722aaa1595.rlib" "/opt/crater/target/debug/deps/libieee754-47d71936b5606ce4.rlib" "/opt/crater/target/debug/deps/libbitflags-87aacccedafc3e9f.rlib" "/opt/crater/target/debug/deps/libbio-784c206c85b7a6eb.rlib" "/opt/crater/target/debug/deps/libfxhash-4124a3dcd49470d3.rlib" "/opt/crater/target/debug/deps/libvec_map-149d3001e0b60fe7.rlib" "/opt/crater/target/debug/deps/libstatrs-386a098639e0e4bf.rlib" "/opt/crater/target/debug/deps/librand-ba84577f1cc5d70c.rlib" "/opt/crater/target/debug/deps/librand-640c68aa6b834c4e.rlib" "/opt/crater/target/debug/deps/libfnv-6e18f98be4338210.rlib" "/opt/crater/target/debug/deps/libbv-e349db919246f342.rlib" "/opt/crater/target/debug/deps/libordered_float-4ac8fd4105c2b159.rlib" "/opt/crater/target/debug/deps/libnum_integer-440f23443e3e87b1.rlib" "/opt/crater/target/debug/deps/libnewtype_derive-50f86e94e5894903.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_num-563bb5ab93ae8895.rlib" "/opt/crater/target/debug/deps/libitertools-42e27b01991a8665.rlib" "/opt/crater/target/debug/deps/libeither-0991b1b51775eba9.rlib" "/opt/crater/target/debug/deps/libcustom_derive-0f45cb4ce8c03868.rlib" "/opt/crater/target/debug/deps/libcsv-dd3c866063c1a99c.rlib" "/opt/crater/target/debug/deps/libryu-a9583eff3872e809.rlib" "/opt/crater/target/debug/deps/libitoa-fbd08118d5c2ed14.rlib" "/opt/crater/target/debug/deps/libcsv_core-e1c4383d785183ec.rlib" "/opt/crater/target/debug/deps/libbstr-a1c7365574e90760.rlib" "/opt/crater/target/debug/deps/libregex_automata-a07793a8fb895fbe.rlib" "/opt/crater/target/debug/deps/libbyteorder-98f71e4258b709b0.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/libapprox-6a6bdd1ea8ffac53.rlib" "/opt/crater/target/debug/deps/libnum_traits-c28daeab5210b49d.rlib" "/opt/crater/target/debug/deps/libbio_types-0ca91003d92025c0.rlib" "/opt/crater/target/debug/deps/libserde-50e5d46514dccf4f.rlib" "/opt/crater/target/debug/deps/libregex-c0027aab54c0528f.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-13b0b3929bf45361.rlib" "/opt/crater/target/debug/deps/libmemchr-49b423f6702d6bce.rlib" "/opt/crater/target/debug/deps/liblibc-1804d2516af09bff.rlib" "/opt/crater/target/debug/deps/liblazy_static-1f7a4359e40a6da9.rlib" "/opt/crater/target/debug/deps/libquick_error-f50ea951eae373ef.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-ef2a4b8ea9f786e7.rlib(rgsl-ef2a4b8ea9f786e7.rgsl.8znepd78-cgu.10.rcgu.o): In function `rgsl::error::erfc': [INFO] [stderr] /opt/crater/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/error.rs:28: undefined reference to `gsl_sf_erfc' [INFO] [stderr] /opt/crater/target/debug/deps/librgsl-ef2a4b8ea9f786e7.rlib(rgsl-ef2a4b8ea9f786e7.rgsl.8znepd78-cgu.13.rcgu.o): In function `rgsl::randist::gaussian::gaussian_pdf': [INFO] [stderr] /opt/crater/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/randist/gaussian.rs:20: undefined reference to `gsl_ran_gaussian_pdf' [INFO] [stderr] /opt/crater/target/debug/deps/librgsl-ef2a4b8ea9f786e7.rlib(rgsl-ef2a4b8ea9f786e7.rgsl.8znepd78-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] 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 `libprosic`. [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [INFO] running `"docker" "inspect" "77a30e3976dc21089c3b4e04fc89cac802e3ba557f4df88ae1ba1648d2551a52"` [INFO] running `"docker" "rm" "-f" "77a30e3976dc21089c3b4e04fc89cac802e3ba557f4df88ae1ba1648d2551a52"` [INFO] [stdout] 77a30e3976dc21089c3b4e04fc89cac802e3ba557f4df88ae1ba1648d2551a52