[INFO] crate libprosic 0.7.3 is already in cache [INFO] testing libprosic-0.7.3 against beta-2020-06-03 for beta-1.45-1 [INFO] extracting crate libprosic 0.7.3 into /workspace/builds/worker-11/source [INFO] validating manifest of crates.io crate libprosic 0.7.3 on toolchain beta-2020-06-03 [INFO] running `"/workspace/cargo-home/bin/cargo" "+beta-2020-06-03" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] started tweaking crates.io crate libprosic 0.7.3 [INFO] finished tweaking crates.io crate libprosic 0.7.3 [INFO] tweaked toml for crates.io crate libprosic 0.7.3 written to /workspace/builds/worker-11/source/Cargo.toml [INFO] running `"/workspace/cargo-home/bin/cargo" "+beta-2020-06-03" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/workspace/cargo-home/bin/cargo" "+beta-2020-06-03" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-06-03" "build" "--frozen"` [INFO] [stdout] bd56a339590b74f2a63fb98a37e98644ee3ac791b4ba4605d1599107aa9d794d [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `"docker" "start" "-a" "bd56a339590b74f2a63fb98a37e98644ee3ac791b4ba4605d1599107aa9d794d"` [INFO] [stderr] sudo: setrlimit(RLIMIT_CORE): Operation not permitted [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling bio v0.24.0 [INFO] [stderr] Compiling ndarray v0.6.10 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling bytecount v0.3.2 [INFO] [stderr] Compiling c_vec v1.0.12 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling cached v0.7.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling lzma-sys v0.1.16 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling GSL v1.1.0 [INFO] [stderr] Compiling itertools v0.7.11 [INFO] [stderr] Compiling itertools v0.5.10 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Compiling num-complex v0.1.43 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling statrs v0.9.0 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling bstr v0.2.13 [INFO] [stderr] Compiling multimap v0.4.0 [INFO] [stderr] Compiling rulinalg v0.2.2 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling clap v2.33.1 [INFO] [stderr] Compiling csv v1.1.3 [INFO] [stderr] Compiling bio-types v0.6.0 [INFO] [stderr] Compiling rusty-machine v0.4.4 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:62:20 [INFO] [stderr] | [INFO] [stderr] 62 | let variants = try!(utils::collect_variants( [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(deprecated)]` on by default [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:70:21 [INFO] [stderr] | [INFO] [stderr] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:75:18 [INFO] [stderr] | [INFO] [stderr] 75 | Some(try!(joint_model.pileup( [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:159:26 [INFO] [stderr] | [INFO] [stderr] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/model/sample.rs:76:17 [INFO] [stderr] | [INFO] [stderr] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stderr] | ^^^ [INFO] [stderr] [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: this warning originates in a macro (in Nightly builds, run with -Z 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 (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: 33 warnings emitted [INFO] [stderr] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 02s [INFO] running `"docker" "inspect" "bd56a339590b74f2a63fb98a37e98644ee3ac791b4ba4605d1599107aa9d794d"` [INFO] running `"docker" "rm" "-f" "bd56a339590b74f2a63fb98a37e98644ee3ac791b4ba4605d1599107aa9d794d"` [INFO] [stdout] bd56a339590b74f2a63fb98a37e98644ee3ac791b4ba4605d1599107aa9d794d [INFO] running `"docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2020-06-03" "test" "--frozen" "--no-run"` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] 1275b1e22bff53aac8b76c539bd35cb1be2ae1d6ac1332062e6ab48a10bab0c0 [INFO] running `"docker" "start" "-a" "1275b1e22bff53aac8b76c539bd35cb1be2ae1d6ac1332062e6ab48a10bab0c0"` [INFO] [stderr] sudo: setrlimit(RLIMIT_CORE): Operation not permitted [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling memchr v0.1.11 [INFO] [stderr] Compiling time v0.1.43 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling thread-id v2.0.0 [INFO] [stderr] Compiling fern v0.4.4 [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:62:20 [INFO] [stderr] | [INFO] [stderr] 62 | let variants = try!(utils::collect_variants( [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(deprecated)]` on by default [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:70:21 [INFO] [stderr] | [INFO] [stderr] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:75:18 [INFO] [stderr] | [INFO] [stderr] 75 | Some(try!(joint_model.pileup( [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:159:26 [INFO] [stderr] | [INFO] [stderr] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/model/sample.rs:76:17 [INFO] [stderr] | [INFO] [stderr] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stderr] | ^^^ [INFO] [stderr] [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: this warning originates in a macro (in Nightly builds, run with -Z 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 (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: 33 warnings emitted [INFO] [stderr] [INFO] [stderr] Compiling aho-corasick v0.5.3 [INFO] [stderr] Compiling thread_local v0.2.7 [INFO] [stderr] Compiling hyper v0.10.16 [INFO] [stderr] Compiling regex v0.1.80 [INFO] [stderr] Compiling flate2 v0.2.20 [INFO] [stderr] Compiling env_logger v0.3.5 [INFO] [stderr] Compiling libprosic v0.7.3 (/opt/rustwide/workdir) [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:62:20 [INFO] [stderr] | [INFO] [stderr] 62 | let variants = try!(utils::collect_variants( [INFO] [stderr] | ^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(deprecated)]` on by default [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:70:21 [INFO] [stderr] | [INFO] [stderr] 70 | let chrom_seq = try!(reference_buffer.seq(&chrom)); [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:75:18 [INFO] [stderr] | [INFO] [stderr] 75 | Some(try!(joint_model.pileup( [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/call/pairwise.rs:159:26 [INFO] [stderr] | [INFO] [stderr] 159 | let mut writer = try!(csv::WriterBuilder::new() [INFO] [stderr] | ^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated item 'try': use the `?` operator instead [INFO] [stderr] --> src/model/sample.rs:76:17 [INFO] [stderr] | [INFO] [stderr] 76 | try!(self.reader.fetch(tid, window_start, end)); [INFO] [stderr] | ^^^ [INFO] [stderr] [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: this warning originates in a macro (in Nightly builds, run with -Z 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 (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stderr] [INFO] [stderr] warning: this method call currently resolves to `<&[T; N] as IntoIterator>::into_iter` (due to autoref coercions), but that might change in the future when `IntoIterator` impls for arrays are added. [INFO] [stderr] --> src/model/sample.rs:612:79 [INFO] [stderr] | [INFO] [stderr] 612 | for (record, true_alt_prob) in records.into_iter().zip(true_alt_probs.into_iter()) { [INFO] [stderr] | ^^^^^^^^^ help: use `.iter()` instead of `.into_iter()` to avoid ambiguity: `iter` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(array_into_iter)]` on by default [INFO] [stderr] = warning: this was previously accepted by the compiler but is being phased out; it will become a hard error in a future release! [INFO] [stderr] = note: for more information, see issue #66145 [INFO] [stderr] [INFO] [stderr] error: linking with `cc` failed: exit code: 1 [INFO] [stderr] | [INFO] [stderr] = note: "cc" "-Wl,--as-needed" "-Wl,-z,noexecstack" "-m64" "-L" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.0.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.1.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.10.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.11.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.12.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.13.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.14.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.15.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.2.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.3.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.4.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.5.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.6.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.7.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.8.rcgu.o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.libprosic.43pjt8j4-cgu.9.rcgu.o" "-o" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96" "/opt/rustwide/target/debug/deps/libprosic-f0e301e90e696c96.25j6eu86wilcb5hd.rcgu.o" "-Wl,--gc-sections" "-pie" "-Wl,-zrelro" "-Wl,-znow" "-nodefaultlibs" "-L" "/opt/rustwide/target/debug/deps" "-L" "/opt/rustwide/target/debug/build/miniz-sys-be9997105ef9946a/out" "-L" "/opt/rustwide/target/debug/build/rust-htslib-86dbd66ddf06a455/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-31bbc74e424dbe8b/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-Wl,-Bstatic" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libtest-0a07979da1fa7aa2.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libterm-171ede43b21d034c.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libgetopts-ea69ac8b5a0936d1.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunicode_width-6be6d4d5d08eb152.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_std-c718480fe68c7cec.rlib" "/opt/rustwide/target/debug/deps/libenv_logger-819f8d9ed2d146bb.rlib" "/opt/rustwide/target/debug/deps/libregex-d82c5a46d17fe99d.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-e6b266851bb808e0.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-c1cad171dbacb223.rlib" "/opt/rustwide/target/debug/deps/libthread_local-5a45baa07faa3424.rlib" "/opt/rustwide/target/debug/deps/libthread_id-c3faa2670c616517.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-45b3dce949e80f6b.rlib" "/opt/rustwide/target/debug/deps/libmemchr-f86894dbc84df200.rlib" "/opt/rustwide/target/debug/deps/libcached-6197903df10fbcfc.rlib" "/opt/rustwide/target/debug/deps/libregex-6cad3429391fd829.rlib" "/opt/rustwide/target/debug/deps/libutf8_ranges-7892513b60c771f1.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-43f5652db6007dc5.rlib" "/opt/rustwide/target/debug/deps/libucd_util-1f813f73804b0485.rlib" "/opt/rustwide/target/debug/deps/libthread_local-c818e360ff3bdad8.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-d32113057ff2e86f.rlib" "/opt/rustwide/target/debug/deps/librusty_machine-fc757e03009bfba1.rlib" "/opt/rustwide/target/debug/deps/librulinalg-4d6d66b880d75caa.rlib" "/opt/rustwide/target/debug/deps/libnum-104529ba3550f7a7.rlib" "/opt/rustwide/target/debug/deps/libnum_iter-b1690be1b5a4a673.rlib" "/opt/rustwide/target/debug/deps/libndarray-75a37da83ec5a474.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-47cef881be71d653.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-4bcc2b9762e7da3a.rlib" "/opt/rustwide/target/debug/deps/libitertools-ad6a7f236e9995ac.rlib" "/opt/rustwide/target/debug/deps/libapprox-784a355a158982c4.rlib" "/opt/rustwide/target/debug/deps/librgsl-d3dc2581de4d5036.rlib" "/opt/rustwide/target/debug/deps/libc_vec-98bc4417a7d1df72.rlib" "/opt/rustwide/target/debug/deps/liblog-38f6b2d55fcb84f2.rlib" "/opt/rustwide/target/debug/deps/liblog-3d65ebee37a7b6c8.rlib" "/opt/rustwide/target/debug/deps/libcfg_if-0d7329a98a9ffead.rlib" "/opt/rustwide/target/debug/deps/librust_htslib-24dbe4b4b7c7be6c.rlib" "/opt/rustwide/target/debug/deps/liblzma_sys-1db241955474320f.rlib" "/opt/rustwide/target/debug/deps/libbzip2_sys-a8e71eeebd133547.rlib" "/opt/rustwide/target/debug/deps/liblibz_sys-111f01d67b58c969.rlib" "/opt/rustwide/target/debug/deps/liblinear_map-eec3d96995b413b9.rlib" "/opt/rustwide/target/debug/deps/liburl-8fcd65f1306150c3.rlib" "/opt/rustwide/target/debug/deps/libpercent_encoding-d4cc324235a66d36.rlib" "/opt/rustwide/target/debug/deps/libidna-d4994925bf4430c7.rlib" "/opt/rustwide/target/debug/deps/libunicode_normalization-467beec5965936c6.rlib" "/opt/rustwide/target/debug/deps/libsmallvec-0ffc8bb136e2289a.rlib" "/opt/rustwide/target/debug/deps/libunicode_bidi-879207079127f333.rlib" "/opt/rustwide/target/debug/deps/libmatches-6c7348f3fc3f1329.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-ee0374dd376fa810.rlib" "/opt/rustwide/target/debug/deps/libitertools-959024ca798a265c.rlib" "/opt/rustwide/target/debug/deps/libieee754-0ec4ca507d084bc4.rlib" "/opt/rustwide/target/debug/deps/libbitflags-b8d615fe970e5edc.rlib" "/opt/rustwide/target/debug/deps/libbio-bfbc08418c9f6e9d.rlib" "/opt/rustwide/target/debug/deps/libfxhash-6fefcd03440aac4a.rlib" "/opt/rustwide/target/debug/deps/libvec_map-4fee75abe813b876.rlib" "/opt/rustwide/target/debug/deps/libstatrs-f248fcfbea588003.rlib" "/opt/rustwide/target/debug/deps/librand-89b1e17aaac01ee5.rlib" "/opt/rustwide/target/debug/deps/librand-f2bda5cbeb1b18df.rlib" "/opt/rustwide/target/debug/deps/liblibc-89d01b793d8b5fe9.rlib" "/opt/rustwide/target/debug/deps/libfnv-d46cc828847a1306.rlib" "/opt/rustwide/target/debug/deps/libbv-50fc3807375a67b1.rlib" "/opt/rustwide/target/debug/deps/libordered_float-040e71447d692b2d.rlib" "/opt/rustwide/target/debug/deps/libnum_integer-e2d76c693688508b.rlib" "/opt/rustwide/target/debug/deps/libnewtype_derive-00c9e54d88f507c9.rlib" "/opt/rustwide/target/debug/deps/libndarray-b5e103f4d73b0b9c.rlib" "/opt/rustwide/target/debug/deps/libnum_complex-bbd1fd552e81a9cb.rlib" "/opt/rustwide/target/debug/deps/libmatrixmultiply-ac76c98d89ba6b62.rlib" "/opt/rustwide/target/debug/deps/librawpointer-17d31d634d793217.rlib" "/opt/rustwide/target/debug/deps/libmultimap-293c69130c17f5bb.rlib" "/opt/rustwide/target/debug/deps/libitertools_num-2b134dc9e6393fb0.rlib" "/opt/rustwide/target/debug/deps/libitertools-9a90d29817c861d5.rlib" "/opt/rustwide/target/debug/deps/libeither-667bb5f36f496548.rlib" "/opt/rustwide/target/debug/deps/libcustom_derive-5ad93899f0b0906c.rlib" "/opt/rustwide/target/debug/deps/libcsv-e0060ba1b9efc656.rlib" "/opt/rustwide/target/debug/deps/libryu-e41edf2aeea0eb4e.rlib" "/opt/rustwide/target/debug/deps/libitoa-6a422fec93b9e5ce.rlib" "/opt/rustwide/target/debug/deps/libcsv_core-98d44476b2b28cf6.rlib" "/opt/rustwide/target/debug/deps/libbstr-8fb0ea270f60a592.rlib" "/opt/rustwide/target/debug/deps/libregex_automata-640879b5b033ad4b.rlib" "/opt/rustwide/target/debug/deps/libbyteorder-78580fbf595daae7.rlib" "/opt/rustwide/target/debug/deps/libbytecount-17868b09601e8f64.rlib" "/opt/rustwide/target/debug/deps/libbit_set-0dba111ac5eac8a1.rlib" "/opt/rustwide/target/debug/deps/libbit_vec-d57af282271f225d.rlib" "/opt/rustwide/target/debug/deps/libapprox-52172897a72429a6.rlib" "/opt/rustwide/target/debug/deps/libnum_traits-447df9d8850f95e5.rlib" "/opt/rustwide/target/debug/deps/libbio_types-323e058bf4cd9c93.rlib" "/opt/rustwide/target/debug/deps/libserde-7740d6aa44a49178.rlib" "/opt/rustwide/target/debug/deps/libregex-9d7abde785476cae.rlib" "/opt/rustwide/target/debug/deps/libthread_local-8d83e4901f0f282f.rlib" "/opt/rustwide/target/debug/deps/libregex_syntax-54fdda16b5257135.rlib" "/opt/rustwide/target/debug/deps/libaho_corasick-0b4c429c60f353ff.rlib" "/opt/rustwide/target/debug/deps/libmemchr-f8260b06e2dd8573.rlib" "/opt/rustwide/target/debug/deps/liblazy_static-36bd8bbfaaa85bd1.rlib" "/opt/rustwide/target/debug/deps/libquick_error-a8ed19302f3259f8.rlib" "-Wl,--start-group" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libstd-44f8eb3d0b2fad61.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libpanic_unwind-abc626f09920d361.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libhashbrown-546e83c8973f1a65.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_alloc-12768dfc68674934.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace-e06867e4497f2ee8.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libbacktrace_sys-cbc579f43f6df57b.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_demangle-7abd6d5a7ebf9a23.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libunwind-46423c7bc03bd327.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcfg_if-fc3773ed7bc68f07.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liblibc-9cdc98176efd27e2.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/liballoc-02d88502a763e06b.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/librustc_std_workspace_core-8cdc9d38dd6cd3ce.rlib" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcore-336f7d63e72901ef.rlib" "-Wl,--end-group" "/opt/rustwide/rustup-home/toolchains/beta-2020-06-03-x86_64-unknown-linux-gnu/lib/rustlib/x86_64-unknown-linux-gnu/lib/libcompiler_builtins-57917b1be5233117.rlib" "-Wl,-Bdynamic" "-llzma" "-lz" "-lutil" "-ldl" "-lutil" "-ldl" "-lrt" "-lpthread" "-lgcc_s" "-lc" "-lm" "-lrt" "-lpthread" "-lutil" "-ldl" "-lutil" [INFO] [stderr] = note: /usr/bin/ld: /opt/rustwide/target/debug/deps/librgsl-d3dc2581de4d5036.rlib(rgsl-d3dc2581de4d5036.rgsl.bwj4uihs-cgu.10.rcgu.o): in function `rgsl::randist::gaussian::gaussian_pdf': [INFO] [stderr] /opt/rustwide/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] /usr/bin/ld: /opt/rustwide/target/debug/deps/librgsl-d3dc2581de4d5036.rlib(rgsl-d3dc2581de4d5036.rgsl.bwj4uihs-cgu.10.rcgu.o): in function `rgsl::randist::gaussian::ugaussian_P': [INFO] [stderr] /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/randist/gaussian.rs:73: undefined reference to `gsl_cdf_ugaussian_P' [INFO] [stderr] /usr/bin/ld: /opt/rustwide/target/debug/deps/librgsl-d3dc2581de4d5036.rlib(rgsl-d3dc2581de4d5036.rgsl.bwj4uihs-cgu.9.rcgu.o): in function `rgsl::error::erfc': [INFO] [stderr] /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/GSL-1.1.0/src/error.rs:28: undefined reference to `gsl_sf_erfc' [INFO] [stderr] collect2: error: ld returned 1 exit status [INFO] [stderr] [INFO] [stderr] [INFO] [stderr] error: aborting due to previous error; 34 warnings emitted [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" "1275b1e22bff53aac8b76c539bd35cb1be2ae1d6ac1332062e6ab48a10bab0c0"` [INFO] running `"docker" "rm" "-f" "1275b1e22bff53aac8b76c539bd35cb1be2ae1d6ac1332062e6ab48a10bab0c0"` [INFO] [stdout] 1275b1e22bff53aac8b76c539bd35cb1be2ae1d6ac1332062e6ab48a10bab0c0