[INFO] crate global-supertrees 0.1.0 is already in cache [INFO] testing global-supertrees-0.1.0 against beta-2019-09-28 for beta-1.39-1 [INFO] extracting crate global-supertrees 0.1.0 into work/builds/worker-4/source [INFO] validating manifest of crates.io crate global-supertrees 0.1.0 on toolchain beta-2019-09-28 [INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+beta-2019-09-28" "read-manifest" "--manifest-path" "Cargo.toml"` [INFO] started tweaking crates.io crate global-supertrees 0.1.0 [INFO] finished tweaking crates.io crate global-supertrees 0.1.0 [INFO] tweaked toml for crates.io crate global-supertrees 0.1.0 written to work/builds/worker-4/source/Cargo.toml [INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+beta-2019-09-28" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"` [INFO] running `"/big/crater/work/cargo-home/bin/cargo" "+beta-2019-09-28" "fetch" "--locked" "--manifest-path" "Cargo.toml"` [INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-4/source:/opt/rustwide/workdir:ro,Z" "-v" "/big/crater/work/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/big/crater/work/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2019-09-28" "build" "--frozen"` [INFO] [stdout] 6f3ea618bf26c659f47197c6abc724ba164bea276a8c44a7a3f896b098c1cae4 [INFO] running `"docker" "start" "-a" "6f3ea618bf26c659f47197c6abc724ba164bea276a8c44a7a3f896b098c1cae4"` [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Compiling num-complex v0.2.3 [INFO] [stderr] Compiling global-supertrees v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:54:92 [INFO] [stderr] | [INFO] [stderr] 54 | pub fn cache_mapping(mapping : &BTreeMap<[u8; 10], u32>, path : &String) -> 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/utils.rs:61:82 [INFO] [stderr] | [INFO] [stderr] 61 | pub fn load_cache_mapping(path : &String) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: unused import: `rayon::prelude` [INFO] [stderr] --> src/tree_merging.rs:2:5 [INFO] [stderr] | [INFO] [stderr] 2 | use rayon::prelude::*; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `trees` [INFO] [stderr] --> src/main.rs:98:9 [INFO] [stderr] | [INFO] [stderr] 98 | let trees : Vec = distance_matrices.par_iter().map(| dm | dm.neighbour_joining()).collect(); [INFO] [stderr] | ^^^^^ help: consider prefixing with an underscore: `_trees` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `distance_matrices` [INFO] [stderr] --> src/tree_merging.rs:10:9 [INFO] [stderr] | [INFO] [stderr] 10 | let distance_matrices: Vec = [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ help: consider prefixing with an underscore: `_distance_matrices` [INFO] [stderr] [INFO] [stderr] warning: function is never used: `merge_distance_matrices` [INFO] [stderr] --> src/tree_merging.rs:102:1 [INFO] [stderr] | [INFO] [stderr] 102 | fn merge_distance_matrices(dms: Vec) -> TreeDistanceMatrix { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 13.65s [INFO] running `"docker" "inspect" "6f3ea618bf26c659f47197c6abc724ba164bea276a8c44a7a3f896b098c1cae4"` [INFO] running `"docker" "rm" "-f" "6f3ea618bf26c659f47197c6abc724ba164bea276a8c44a7a3f896b098c1cae4"` [INFO] [stdout] 6f3ea618bf26c659f47197c6abc724ba164bea276a8c44a7a3f896b098c1cae4 [INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-4/source:/opt/rustwide/workdir:ro,Z" "-v" "/big/crater/work/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/big/crater/work/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2019-09-28" "test" "--frozen" "--no-run"` [INFO] [stdout] 433c6db1cfd1aa200f1d427daeba4924bd589c564f8e0b6f6ec668ce69d464df [INFO] running `"docker" "start" "-a" "433c6db1cfd1aa200f1d427daeba4924bd589c564f8e0b6f6ec668ce69d464df"` [INFO] [stderr] Compiling global-supertrees v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stderr] --> src/utils.rs:54:92 [INFO] [stderr] | [INFO] [stderr] 54 | pub fn cache_mapping(mapping : &BTreeMap<[u8; 10], u32>, path : &String) -> 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/utils.rs:61:82 [INFO] [stderr] | [INFO] [stderr] 61 | pub fn load_cache_mapping(path : &String) -> Result, Box> { [INFO] [stderr] | ^^^^^ help: use `dyn`: `dyn Error` [INFO] [stderr] [INFO] [stderr] warning: unused import: `rayon::prelude` [INFO] [stderr] --> src/tree_merging.rs:2:5 [INFO] [stderr] | [INFO] [stderr] 2 | use rayon::prelude::*; [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_imports)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `trees` [INFO] [stderr] --> src/main.rs:98:9 [INFO] [stderr] | [INFO] [stderr] 98 | let trees : Vec = distance_matrices.par_iter().map(| dm | dm.neighbour_joining()).collect(); [INFO] [stderr] | ^^^^^ help: consider prefixing with an underscore: `_trees` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `distance_matrices` [INFO] [stderr] --> src/tree_merging.rs:10:9 [INFO] [stderr] | [INFO] [stderr] 10 | let distance_matrices: Vec = [INFO] [stderr] | ^^^^^^^^^^^^^^^^^ help: consider prefixing with an underscore: `_distance_matrices` [INFO] [stderr] [INFO] [stderr] warning: function is never used: `merge_distance_matrices` [INFO] [stderr] --> src/tree_merging.rs:102:1 [INFO] [stderr] | [INFO] [stderr] 102 | fn merge_distance_matrices(dms: Vec) -> TreeDistanceMatrix { [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 2.94s [INFO] running `"docker" "inspect" "433c6db1cfd1aa200f1d427daeba4924bd589c564f8e0b6f6ec668ce69d464df"` [INFO] running `"docker" "rm" "-f" "433c6db1cfd1aa200f1d427daeba4924bd589c564f8e0b6f6ec668ce69d464df"` [INFO] [stdout] 433c6db1cfd1aa200f1d427daeba4924bd589c564f8e0b6f6ec668ce69d464df [INFO] running `"docker" "create" "-v" "/big/crater/work/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/big/crater/work/builds/worker-4/source:/opt/rustwide/workdir:ro,Z" "-v" "/big/crater/work/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/big/crater/work/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=warn" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2019-09-28" "test" "--frozen"` [INFO] [stdout] 695ea7308be25039fbfa7a52b17c5244c658ad02c92af057db67247356258103 [INFO] running `"docker" "start" "-a" "695ea7308be25039fbfa7a52b17c5244c658ad02c92af057db67247356258103"` [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 0.02s [INFO] [stderr] Running /opt/rustwide/target/debug/deps/global_supertrees-a6dcbdb41e28c858 [INFO] [stdout] [INFO] [stdout] running 16 tests [INFO] [stdout] test tests::tests::test_find_first_zero ... ok [INFO] [stdout] test tests::tests::test_find_first_common_ancestor ... ok [INFO] [stdout] test test_tree_parsing::tests::test_construct_tree_from_file_3 ... ok [INFO] [stdout] test tests::tests::test_load_tree_file ... ok [INFO] [stdout] test test_tree_parsing::tests::test_construct_tree_from_file_2 ... ok [INFO] [stdout] test test_tree_parsing::tests::test_construct_tree_from_file_1 ... ok [INFO] [stdout] test tests::tests::test_get_levels_from_root ... ok [INFO] [stdout] test tests::tests::test_to_dot ... ok [INFO] [stdout] test tests::tests::test_merge_organisms ... FAILED [INFO] [stdout] test tests::tests::test_batch_id_tax_mapping ... FAILED [INFO] [stdout] test tests::tests::test_to_distance_matrix_medium ... ok [INFO] [stdout] test tests::tests::test_to_distance_matrix_medium_nested ... ok [INFO] [stdout] test tests::tests::test_get_partial_tree ... ok [INFO] [stdout] test tests::tests::test_to_distance_matrix_simple ... ok [INFO] [stdout] test tests::tests::test_neighbour_joining ... ok [INFO] [stdout] test tests::tests::test_tree_merging ... ok [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] [INFO] [stdout] ---- tests::tests::test_merge_organisms stdout ---- [INFO] [stdout] thread 'tests::tests::test_merge_organisms' panicked at 'file not found: Os { code: 2, kind: NotFound, message: "No such file or directory" }', src/libcore/result.rs:1165:5 [INFO] [stdout] note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace. [INFO] [stdout] [INFO] [stdout] ---- tests::tests::test_batch_id_tax_mapping stdout ---- [INFO] [stdout] thread 'tests::tests::test_batch_id_tax_mapping' panicked at 'file not found: Os { code: 2, kind: NotFound, message: "No such file or directory" }', src/libcore/result.rs:1165:5 [INFO] [stdout] stack backtrace: [INFO] [stdout] 0: 0x55cb46a953f4 - backtrace::backtrace::libunwind::trace::hf625d18232cbbbd4 [INFO] [stdout] at /cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.37/src/backtrace/libunwind.rs:88 [INFO] [stdout] 1: 0x55cb46a953f4 - backtrace::backtrace::trace_unsynchronized::h41d74150fc6ff542 [INFO] [stdout] at /cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.37/src/backtrace/mod.rs:66 [INFO] [stdout] 2: 0x55cb46a953f4 - std::sys_common::backtrace::_print_fmt::h85d37830c667a1f9 [INFO] [stdout] at src/libstd/sys_common/backtrace.rs:76 [INFO] [stdout] 3: 0x55cb46a953f4 - ::fmt::h2b7ac01d5feaf9b2 [INFO] [stdout] at src/libstd/sys_common/backtrace.rs:60 [INFO] [stdout] 4: 0x55cb46ab58ec - core::fmt::write::h7fd0d904495c035f [INFO] [stdout] at src/libcore/fmt/mod.rs:1030 [INFO] [stdout] 5: 0x55cb467d2825 - std::io::Write::write_fmt::h424452e6ba861394 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/io/mod.rs:1412 [INFO] [stdout] 6: 0x55cb46a90f71 - std::io::impls::>::write_fmt::h814a51d8ae1dee4a [INFO] [stdout] at src/libstd/io/impls.rs:141 [INFO] [stdout] 7: 0x55cb46a97915 - std::sys_common::backtrace::_print::h4c743f7c274a5a74 [INFO] [stdout] at src/libstd/sys_common/backtrace.rs:64 [INFO] [stdout] 8: 0x55cb46a97915 - std::sys_common::backtrace::print::ha5c4f4bf03800d4d [INFO] [stdout] at src/libstd/sys_common/backtrace.rs:49 [INFO] [stdout] 9: 0x55cb46a97915 - std::panicking::default_hook::{{closure}}::h8b842185774c09e6 [INFO] [stdout] at src/libstd/panicking.rs:196 [INFO] [stdout] 10: 0x55cb46a9759c - std::panicking::default_hook::hd8ec13ee1bc2a65a [INFO] [stdout] at src/libstd/panicking.rs:207 [INFO] [stdout] 11: 0x55cb46a98015 - std::panicking::rust_panic_with_hook::hf3b27166e5f403e7 [INFO] [stdout] at src/libstd/panicking.rs:473 [INFO] [stdout] 12: 0x55cb46a97bb2 - std::panicking::continue_panic_fmt::hd961751be84a6f83 [INFO] [stdout] at src/libstd/panicking.rs:380 [INFO] [stdout] 13: 0x55cb46a97aa6 - rust_begin_unwind [INFO] [stdout] at src/libstd/panicking.rs:307 [INFO] [stdout] 14: 0x55cb46ab238a - core::panicking::panic_fmt::h467e0364f9237670 [INFO] [stdout] at src/libcore/panicking.rs:85 [INFO] [stdout] 15: 0x55cb46ab2487 - core::result::unwrap_failed::h38f3a56f1dadf080 [INFO] [stdout] at src/libcore/result.rs:1165 [INFO] [stdout] 16: 0x55cb467cb738 - core::result::Result::expect::h184bff5108493be8 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libcore/result.rs:960 [INFO] [stdout] 17: 0x55cb467d171d - global_supertrees::uniprot::load_mapping_file::h84617ca70f8dcaaf [INFO] [stdout] at src/uniprot.rs:34 [INFO] [stdout] 18: 0x55cb46715e34 - global_supertrees::tests::tests::test_batch_id_tax_mapping::h11d4eb7ffaaf58a9 [INFO] [stdout] at src/tests.rs:230 [INFO] [stdout] 19: 0x55cb46715cea - global_supertrees::tests::tests::test_batch_id_tax_mapping::{{closure}}::h384bb8fab36cd00d [INFO] [stdout] at src/tests.rs:227 [INFO] [stdout] 20: 0x55cb467b5dce - core::ops::function::FnOnce::call_once::h17614883a6f736b1 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libcore/ops/function.rs:227 [INFO] [stdout] 21: 0x55cb467dc71f - as core::ops::function::FnOnce>::call_once::h8b428e8a43aaf8e9 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/liballoc/boxed.rs:922 [INFO] [stdout] 22: 0x55cb46a9ab9a - __rust_maybe_catch_panic [INFO] [stdout] at src/libpanic_unwind/lib.rs:80 [INFO] [stdout] 23: 0x55cb467f6f2e - std::panicking::try::heccce20d527a3513 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/panicking.rs:271 [INFO] [stdout] 24: 0x55cb467f6f2e - std::panic::catch_unwind::h7fd8f5d3271f1692 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/panic.rs:394 [INFO] [stdout] 25: 0x55cb467f6f2e - test::run_test::run_test_inner::{{closure}}::h88b46e5c359957e5 [INFO] [stdout] at src/libtest/lib.rs:1413 [INFO] [stdout] 26: 0x55cb467d1f95 - std::sys_common::backtrace::__rust_begin_short_backtrace::h00847676c8212941 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/sys_common/backtrace.rs:126 [INFO] [stdout] 27: 0x55cb467d6125 - std::thread::Builder::spawn_unchecked::{{closure}}::{{closure}}::h5dd37acd2295488e [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/thread/mod.rs:470 [INFO] [stdout] 28: 0x55cb467d6125 - as core::ops::function::FnOnce<()>>::call_once::h9d32b103da0b97c6 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/panic.rs:315 [INFO] [stdout] 29: 0x55cb467d6125 - std::panicking::try::do_call::h2bd819a3056c57cd [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/panicking.rs:292 [INFO] [stdout] 30: 0x55cb46a9ab9a - __rust_maybe_catch_panic [INFO] [stdout] at src/libpanic_unwind/lib.rs:80 [INFO] [stdout] 31: 0x55cb467d66d2 - std::panicking::try::h243a25457a848a1a [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/panicking.rs:271 [INFO] [stdout] 32: 0x55cb467d66d2 - std::panic::catch_unwind::h74b81f55e55e757c [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/panic.rs:394 [INFO] [stdout] 33: 0x55cb467d66d2 - std::thread::Builder::spawn_unchecked::{{closure}}::h4c2d214a2cffa6cf [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libstd/thread/mod.rs:469 [INFO] [stdout] 34: 0x55cb467d66d2 - core::ops::function::FnOnce::call_once{{vtable.shim}}::h8a8a187b3fb58e53 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/libcore/ops/function.rs:227 [INFO] [stdout] 35: 0x55cb46a8d94f - as core::ops::function::FnOnce>::call_once::h3cdef3b7ea22cd61 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/liballoc/boxed.rs:922 [INFO] [stdout] 36: 0x55cb46a99f90 - as core::ops::function::FnOnce>::call_once::hc8f25720bf0d5424 [INFO] [stdout] at /rustc/5752b6348ee6971573b278c315a02193c847ee32/src/liballoc/boxed.rs:922 [INFO] [stdout] 37: 0x55cb46a99f90 - std::sys_common::thread::start_thread::h7e8885ccfd5d1932 [INFO] [stdout] at src/libstd/sys_common/thread.rs:13 [INFO] [stdout] 38: 0x55cb46a99f90 - std::sys::unix::thread::Thread::new::thread_start::h5d24df932d688baf [INFO] [stdout] at src/libstd/sys/unix/thread.rs:79 [INFO] [stdout] 39: 0x7f833b5c76db - start_thread [INFO] [stdout] 40: 0x7f833b0d888f - __clone [INFO] [stdout] 41: 0x0 - [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] tests::tests::test_batch_id_tax_mapping [INFO] [stdout] tests::tests::test_merge_organisms [INFO] [stdout] [INFO] [stdout] test result: FAILED. 14 passed; 2 failed; 0 ignored; 0 measured; 0 filtered out [INFO] [stdout] [INFO] [stderr] error: test failed, to rerun pass '--bin global-supertrees' [INFO] running `"docker" "inspect" "695ea7308be25039fbfa7a52b17c5244c658ad02c92af057db67247356258103"` [INFO] running `"docker" "rm" "-f" "695ea7308be25039fbfa7a52b17c5244c658ad02c92af057db67247356258103"` [INFO] [stdout] 695ea7308be25039fbfa7a52b17c5244c658ad02c92af057db67247356258103