[INFO] fetching crate biofile 1.10.3... [INFO] checking biofile-1.10.3 against try#a7a572ce3edd6d476191fbfe92c9c1986e009b34 for pr-87190-3 [INFO] extracting crate biofile 1.10.3 into /workspace/builds/worker-78/source [INFO] validating manifest of crates.io crate biofile 1.10.3 on toolchain a7a572ce3edd6d476191fbfe92c9c1986e009b34 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate biofile 1.10.3 [INFO] finished tweaking crates.io crate biofile 1.10.3 [INFO] tweaked toml for crates.io crate biofile 1.10.3 written to /workspace/builds/worker-78/source/Cargo.toml [INFO] crate crates.io crate biofile 1.10.3 already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-78/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-78/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" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 3e935d810f849dafbe46cd076205627faba9b8904f02ba42a06e6ec96c40e321 [INFO] running `Command { std: "docker" "start" "-a" "3e935d810f849dafbe46cd076205627faba9b8904f02ba42a06e6ec96c40e321", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "3e935d810f849dafbe46cd076205627faba9b8904f02ba42a06e6ec96c40e321", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "3e935d810f849dafbe46cd076205627faba9b8904f02ba42a06e6ec96c40e321", kill_on_drop: false }` [INFO] [stdout] 3e935d810f849dafbe46cd076205627faba9b8904f02ba42a06e6ec96c40e321 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-78/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-78/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" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 6b80a3dc1c9ae1582e1a3882cf2fd89d45a0c64b89685be21f814b5522397b58 [INFO] running `Command { std: "docker" "start" "-a" "6b80a3dc1c9ae1582e1a3882cf2fd89d45a0c64b89685be21f814b5522397b58", kill_on_drop: false }` [INFO] [stderr] Copying to /tmp/fixit [INFO] [stderr] Running `cargo fix --edition` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling autocfg v0.1.6 [INFO] [stderr] Compiling libc v0.2.62 [INFO] [stderr] Compiling semver-parser v0.7.0 [INFO] [stderr] Checking rand_core v0.4.2 [INFO] [stderr] Compiling getrandom v0.1.12 [INFO] [stderr] Compiling arrayvec v0.4.11 [INFO] [stderr] Checking nodrop v0.1.13 [INFO] [stderr] Checking either v1.5.3 [INFO] [stderr] Checking scopeguard v1.0.0 [INFO] [stderr] Checking ppv-lite86 v0.2.5 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling rayon-core v1.6.0 [INFO] [stderr] Compiling bitflags v1.2.0 [INFO] [stderr] Checking rawpointer v0.1.0 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Checking crossbeam-utils v0.6.6 [INFO] [stderr] Checking itertools v0.7.11 [INFO] [stderr] Compiling semver v0.9.0 [INFO] [stderr] Checking rand_core v0.3.1 [INFO] [stderr] Checking rand_jitter v0.1.4 [INFO] [stderr] Checking crossbeam-queue v0.1.2 [INFO] [stderr] Checking c2-chacha v0.2.2 [INFO] [stderr] Checking rand_xorshift v0.1.1 [INFO] [stderr] Checking rand_hc v0.1.0 [INFO] [stderr] Checking rand_isaac v0.1.1 [INFO] [stderr] Compiling num-traits v0.2.8 [INFO] [stderr] Compiling num-integer v0.1.41 [INFO] [stderr] Compiling num-complex v0.2.3 [INFO] [stderr] Compiling num-bigint v0.2.3 [INFO] [stderr] Compiling num-rational v0.2.2 [INFO] [stderr] Compiling num-iter v0.1.39 [INFO] [stderr] Compiling rand_pcg v0.1.2 [INFO] [stderr] Compiling rand_chacha v0.1.1 [INFO] [stderr] Compiling rand v0.6.5 [INFO] [stderr] Compiling rustc_version v0.2.3 [INFO] [stderr] Compiling memoffset v0.5.1 [INFO] [stderr] Checking crossbeam-epoch v0.7.2 [INFO] [stderr] Checking num_cpus v1.10.1 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking rand_os v0.1.3 [INFO] [stderr] Checking clap v2.33.3 [INFO] [stderr] Checking crossbeam-deque v0.7.1 [INFO] [stderr] Checking rand_core v0.5.1 [INFO] [stderr] Checking rand_chacha v0.2.1 [INFO] [stderr] Checking rand v0.7.2 [INFO] [stderr] Checking rayon v1.2.0 [INFO] [stderr] Checking tempfile v3.1.0 [INFO] [stderr] Checking num v0.2.0 [INFO] [stderr] Checking math v0.10.0 [INFO] [stderr] Checking program-flow v0.1.3 [INFO] [stderr] Checking ndarray-rand v0.9.0 [INFO] [stderr] Checking biofile v1.10.3 (/tmp/fixit) [INFO] [stderr] Migrating src/lib.rs from 2018 edition to 2021 [INFO] [stderr] Fixed src/peak_file.rs (1 fix) [INFO] [stderr] Fixed src/plink_bed/plink_snps.rs (1 fix) [INFO] [stdout] warning: the feature `bufreader_seek_relative` has been stable since 1.53.0 and no longer requires an attribute to enable [INFO] [stdout] --> src/lib.rs:1:12 [INFO] [stdout] | [INFO] [stdout] 1 | #![feature(bufreader_seek_relative)] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(stable_features)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Migrating src/bin/collate_paired_end.rs from 2018 edition to 2021 [INFO] [stderr] warning: failed to automatically apply fixes suggested by rustc to crate `biofile` [INFO] [stderr] [INFO] [stderr] after fixes were automatically applied the compiler reported errors within these files: [INFO] [stderr] [INFO] [stderr] * src/bed.rs [INFO] [stderr] * src/bedgraph.rs [INFO] [stderr] [INFO] [stderr] This likely indicates a bug in either rustc or cargo itself, [INFO] [stderr] and we would appreciate a bug report! You're likely to see [INFO] [stderr] a number of compiler warnings after this message which cargo [INFO] [stderr] attempted to fix but failed. If you could open an issue at [INFO] [stderr] https://github.com/rust-lang/rust/issues [INFO] [stderr] quoting the full output of this command we'd be very appreciative! [INFO] [stderr] Note that you may be able to make some more progress in the near-term [INFO] [stderr] fixing code with the `--broken-code` flag [INFO] [stderr] [INFO] [stderr] The following errors were reported: [INFO] [stderr] error[E0107]: missing generics for trait `ToChromIntervalValueIter` [INFO] [stderr] --> src/bed.rs:282:22 [INFO] [stderr] | [INFO] [stderr] 282 | ::get_chrom_to_interval_to_val( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ expected 4 generic arguments [INFO] [stderr] | [INFO] [stderr] note: trait defined here, with 4 generic parameters: `I`, `C`, `T`, `V` [INFO] [stderr] --> src/iter.rs:18:11 [INFO] [stderr] | [INFO] [stderr] 18 | pub trait ToChromIntervalValueIter [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ - - - - [INFO] [stderr] help: add missing generic arguments [INFO] [stderr] | [INFO] [stderr] 282 | >::get_chrom_to_interval_to_val( [INFO] [stderr] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [INFO] [stderr] [INFO] [stderr] error[E0107]: missing generics for trait `ToChromIntervalValueIter` [INFO] [stderr] --> src/bed.rs:326:22 [INFO] [stderr] | [INFO] [stderr] 326 | ::get_chrom_to_interval_to_val( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ expected 4 generic arguments [INFO] [stderr] | [INFO] [stderr] note: trait defined here, with 4 generic parameters: `I`, `C`, `T`, `V` [INFO] [stderr] --> src/iter.rs:18:11 [INFO] [stderr] | [INFO] [stderr] 18 | pub trait ToChromIntervalValueIter [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ - - - - [INFO] [stderr] help: add missing generic arguments [INFO] [stderr] | [INFO] [stderr] 326 | >::get_chrom_to_interval_to_val( [INFO] [stderr] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [INFO] [stderr] [INFO] [stderr] error[E0107]: missing generics for trait `ToChromIntervalValueIter` [INFO] [stderr] --> src/bedgraph.rs:196:18 [INFO] [stderr] | [INFO] [stderr] 196 | ::get_chrom_to_interval_to_val( [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ expected 4 generic arguments [INFO] [stderr] | [INFO] [stderr] note: trait defined here, with 4 generic parameters: `I`, `C`, `T`, `V` [INFO] [stderr] --> src/iter.rs:18:11 [INFO] [stderr] | [INFO] [stderr] 18 | pub trait ToChromIntervalValueIter [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^ - - - - [INFO] [stderr] help: add missing generic arguments [INFO] [stderr] | [INFO] [stderr] 196 | >::get_chrom_to_interval_to_val( [INFO] [stderr] | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [INFO] [stderr] [INFO] [stderr] error: aborting due to 3 previous errors [INFO] [stderr] [INFO] [stderr] For more information about this error, try `rustc --explain E0107`. [INFO] [stderr] Original diagnostics will follow. [INFO] [stderr] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/bed.rs:282:17 [INFO] [stdout] | [INFO] [stdout] 282 | ToChromIntervalValueIter::get_chrom_to_interval_to_val( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `` [INFO] [stdout] | [INFO] [stdout] = note: `--force-warn bare-trait-objects` implied by `--force-warn rust-2021-compatibility` [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2018) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/bed.rs:326:17 [INFO] [stdout] | [INFO] [stdout] 326 | ToChromIntervalValueIter::get_chrom_to_interval_to_val( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `` [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2018) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/bedgraph.rs:196:13 [INFO] [stdout] | [INFO] [stdout] 196 | ToChromIntervalValueIter::get_chrom_to_interval_to_val( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: use `dyn`: `` [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2018) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `val` [INFO] [stdout] --> src/traits/trait_impl.rs:45:41 [INFO] [stdout] | [INFO] [stdout] 45 | let (chrom, start, end, val) = [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_val` [INFO] [stdout] ... [INFO] [stdout] 55 | test_data_line!("chr1", 2, 10, None::); [INFO] [stdout] | -------------------------------------------- in this macro invocation [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] = note: this warning originates in the macro `test_data_line` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `val` [INFO] [stdout] --> src/traits/trait_impl.rs:45:41 [INFO] [stdout] | [INFO] [stdout] 45 | let (chrom, start, end, val) = [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_val` [INFO] [stdout] ... [INFO] [stdout] 56 | test_data_line!("chrX", 200, 201, Some(19i32)); [INFO] [stdout] | ----------------------------------------------- in this macro invocation [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in the macro `test_data_line` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `val` [INFO] [stdout] --> src/traits/trait_impl.rs:45:41 [INFO] [stdout] | [INFO] [stdout] 45 | let (chrom, start, end, val) = [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_val` [INFO] [stdout] ... [INFO] [stdout] 57 | test_data_line!("chrY", 100, 4000, Some(-2i32)); [INFO] [stdout] | ------------------------------------------------ in this macro invocation [INFO] [stdout] | [INFO] [stdout] = note: this warning originates in the macro `test_data_line` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the feature `bufreader_seek_relative` has been stable since 1.53.0 and no longer requires an attribute to enable [INFO] [stdout] --> src/lib.rs:1:12 [INFO] [stdout] | [INFO] [stdout] 1 | #![feature(bufreader_seek_relative)] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(stable_features)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 7 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 13.53s [INFO] [stderr] Running `cargo check` to verify 2021 [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Checking biofile v1.10.3 (/tmp/fixit) [INFO] [stdout] error[E0783]: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/bed.rs:282:17 [INFO] [stdout] | [INFO] [stdout] 282 | ToChromIntervalValueIter::get_chrom_to_interval_to_val( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: : `use `dyn`` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0783]: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/bed.rs:326:17 [INFO] [stdout] | [INFO] [stdout] 326 | ToChromIntervalValueIter::get_chrom_to_interval_to_val( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: : `use `dyn`` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0783]: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/bedgraph.rs:196:13 [INFO] [stdout] | [INFO] [stdout] 196 | ToChromIntervalValueIter::get_chrom_to_interval_to_val( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: : `use `dyn`` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the feature `bufreader_seek_relative` has been stable since 1.53.0 and no longer requires an attribute to enable [INFO] [stdout] --> src/lib.rs:1:12 [INFO] [stdout] | [INFO] [stdout] 1 | #![feature(bufreader_seek_relative)] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(stable_features)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0783`. [INFO] [stdout] [INFO] [stderr] error: could not compile `biofile` due to 4 previous errors [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stderr] error: build failed [INFO] [stderr] error: failed to check after updating to 2021 [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `cargo check --frozen --all --all-targets --message-format=json` (exit status: 101) [INFO] running `Command { std: "docker" "inspect" "6b80a3dc1c9ae1582e1a3882cf2fd89d45a0c64b89685be21f814b5522397b58", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6b80a3dc1c9ae1582e1a3882cf2fd89d45a0c64b89685be21f814b5522397b58", kill_on_drop: false }` [INFO] [stdout] 6b80a3dc1c9ae1582e1a3882cf2fd89d45a0c64b89685be21f814b5522397b58