[INFO] fetching crate rustybam 0.1.29... [INFO] testing rustybam-0.1.29 against 1.60.0 for beta-1.61-1 [INFO] extracting crate rustybam 0.1.29 into /workspace/builds/worker-23/source [INFO] validating manifest of crates.io crate rustybam 0.1.29 on toolchain 1.60.0 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.60.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] removed /workspace/builds/worker-23/source/.cargo/config [INFO] started tweaking crates.io crate rustybam 0.1.29 [INFO] finished tweaking crates.io crate rustybam 0.1.29 [INFO] tweaked toml for crates.io crate rustybam 0.1.29 written to /workspace/builds/worker-23/source/Cargo.toml [INFO] crate crates.io crate rustybam 0.1.29 already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.60.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] warning: file found to be present in multiple build targets: /workspace/builds/worker-23/source/src/main.rs [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded natord v1.0.9 [INFO] [stderr] Downloaded needletail v0.4.1 [INFO] [stderr] Downloaded libdeflater v0.7.5 [INFO] [stderr] Downloaded calmio_filters v0.1.0 [INFO] [stderr] Downloaded multimap v0.8.3 [INFO] [stderr] Downloaded clap_complete v3.1.1 [INFO] [stderr] Downloaded calm_io v0.1.1 [INFO] [stderr] Downloaded bio-types v0.12.1 [INFO] [stderr] Downloaded bimap v0.6.2 [INFO] [stderr] Downloaded clap_generate v3.0.3 [INFO] [stderr] Downloaded derive-new v0.5.9 [INFO] [stderr] Downloaded bio v0.39.2 [INFO] [stderr] Downloaded enum-map v1.1.1 [INFO] [stderr] Downloaded rust-htslib v0.38.2 [INFO] [stderr] Downloaded libdeflate-sys v0.7.5 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded enum-map-derive v0.6.0 [INFO] [stderr] Downloaded gzp v0.9.5 [INFO] [stderr] Downloaded hts-sys v2.0.2 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 867b662a235de75f28f9c06c7cb020017d6600bc8ecbcc0fe912d38af6d0cda0 [INFO] running `Command { std: "docker" "start" "-a" "867b662a235de75f28f9c06c7cb020017d6600bc8ecbcc0fe912d38af6d0cda0", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "867b662a235de75f28f9c06c7cb020017d6600bc8ecbcc0fe912d38af6d0cda0", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "867b662a235de75f28f9c06c7cb020017d6600bc8ecbcc0fe912d38af6d0cda0", kill_on_drop: false }` [INFO] [stdout] 867b662a235de75f28f9c06c7cb020017d6600bc8ecbcc0fe912d38af6d0cda0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/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=warn" "-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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 895ce35213b877cb59bb70bb500653480225f91899b5c7363f71d578fd6a6b03 [INFO] running `Command { std: "docker" "start" "-a" "895ce35213b877cb59bb70bb500653480225f91899b5c7363f71d578fd6a6b03", kill_on_drop: false }` [INFO] [stderr] warning: file found to be present in multiple build targets: /opt/rustwide/workdir/src/main.rs [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] Compiling syn v1.0.86 [INFO] [stderr] Compiling crossbeam-utils v0.8.7 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling log v0.4.14 [INFO] [stderr] Compiling rustversion v1.0.6 [INFO] [stderr] Compiling crossbeam-epoch v0.9.7 [INFO] [stderr] Compiling unicode-segmentation v1.9.0 [INFO] [stderr] Compiling crc32fast v1.3.2 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling futures-core v0.3.21 [INFO] [stderr] Compiling humantime v2.1.0 [INFO] [stderr] Compiling adler v1.0.2 [INFO] [stderr] Compiling anyhow v1.0.56 [INFO] [stderr] Compiling futures-sink v0.3.21 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling fixedbitset v0.4.1 [INFO] [stderr] Compiling safemem v0.3.3 [INFO] [stderr] Compiling bit-vec v0.6.3 [INFO] [stderr] Compiling bytecount v0.6.2 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling strum v0.23.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling natord v1.0.9 [INFO] [stderr] Compiling bimap v0.6.2 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling memoffset v0.6.5 [INFO] [stderr] Compiling miniz_oxide v0.4.4 [INFO] [stderr] Compiling rayon v1.5.1 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling lock_api v0.4.6 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling jobserver v0.1.24 [INFO] [stderr] Compiling getrandom v0.2.5 [INFO] [stderr] Compiling num_cpus v1.13.1 [INFO] [stderr] Compiling regex v1.5.5 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling ordered-float v1.1.1 [INFO] [stderr] Compiling colored v2.0.0 [INFO] [stderr] Compiling bit-set v0.5.2 [INFO] [stderr] Compiling petgraph v0.6.0 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling spin v0.9.2 [INFO] [stderr] Compiling cc v1.0.73 [INFO] [stderr] Compiling core_affinity v0.5.10 [INFO] [stderr] Compiling rand_core v0.6.3 [INFO] [stderr] Compiling nanorand v0.6.1 [INFO] [stderr] Compiling buf_redux v0.8.4 [INFO] [stderr] Compiling heck v0.3.3 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling env_logger v0.9.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling crossbeam-channel v0.5.2 [INFO] [stderr] Compiling num-rational v0.4.0 [INFO] [stderr] Compiling ndarray v0.15.4 [INFO] [stderr] Compiling chrono v0.4.19 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling cmake v0.1.48 [INFO] [stderr] Compiling openssl-src v111.17.0+1.1.1m [INFO] [stderr] Compiling crossbeam-deque v0.8.1 [INFO] [stderr] Compiling rayon-core v1.9.1 [INFO] [stderr] Compiling libz-sys v1.1.5 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling openssl-sys v0.9.72 [INFO] [stderr] Compiling curl-sys v0.4.52+curl-7.81.0 [INFO] [stderr] Compiling libdeflate-sys v0.7.5 [INFO] [stderr] Compiling hts-sys v2.0.2 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling bzip2 v0.4.3 [INFO] [stderr] Compiling xz2 v0.1.6 [INFO] [stderr] Compiling libdeflater v0.7.5 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling serde_derive v1.0.136 [INFO] [stderr] Compiling thiserror-impl v1.0.30 [INFO] [stderr] Compiling clap_derive v3.1.4 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling pin-project-internal v1.0.10 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling strum_macros v0.23.1 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Compiling calmio_filters v0.1.0 [INFO] [stderr] Compiling calm_io v0.1.1 [INFO] [stderr] Compiling nalgebra v0.27.1 [INFO] [stderr] Compiling enum-map v1.1.1 [INFO] [stderr] Compiling thiserror v1.0.30 [INFO] [stderr] Compiling pin-project v1.0.10 [INFO] [stderr] Compiling bio-types v0.12.1 [INFO] [stderr] Compiling flume v0.10.11 [INFO] [stderr] Compiling clap v3.1.6 [INFO] [stderr] Compiling serde v1.0.136 [INFO] [stderr] Compiling flate2 v1.0.22 [INFO] [stderr] Compiling clap_complete v3.1.1 [INFO] [stderr] Compiling gzp v0.9.5 [INFO] [stderr] Compiling needletail v0.4.1 [INFO] [stderr] Compiling clap_generate v3.0.3 [INFO] [stderr] Compiling rustybam v0.1.29 (/opt/rustwide/workdir) [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::PropagateVersion`: Replaced with `Command::propagate_version` and `Command::is_propagate_version_set` [INFO] [stdout] --> src/cli.rs:5:36 [INFO] [stdout] | [INFO] [stdout] 5 | #[clap(global_setting(AppSettings::PropagateVersion))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::InferSubcommands`: Replaced with `Command::infer_subcommands` [INFO] [stdout] --> src/cli.rs:7:36 [INFO] [stdout] | [INFO] [stdout] 7 | #[clap(global_setting(AppSettings::InferSubcommands))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::HelpExpected`: Replaced with `Command::help_expected` [INFO] [stdout] --> src/cli.rs:8:36 [INFO] [stdout] | [INFO] [stdout] 8 | #[clap(global_setting(AppSettings::HelpExpected))] [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::SubcommandRequiredElseHelp`: Replaced with `Command::subcommand_required` combined with `Command::arg_required_else_help` [INFO] [stdout] --> src/cli.rs:9:29 [INFO] [stdout] | [INFO] [stdout] 9 | #[clap(setting(AppSettings::SubcommandRequiredElseHelp))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling bstr v0.2.17 [INFO] [stderr] Compiling multimap v0.8.3 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling csv v1.1.6 [INFO] [stderr] Compiling rust-htslib v0.38.2 [INFO] [stderr] Compiling statrs v0.15.0 [INFO] [stderr] Compiling bio v0.39.2 [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::PropagateVersion`: Replaced with `Command::propagate_version` and `Command::is_propagate_version_set` [INFO] [stdout] --> src/cli.rs:5:36 [INFO] [stdout] | [INFO] [stdout] 5 | #[clap(global_setting(AppSettings::PropagateVersion))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::InferSubcommands`: Replaced with `Command::infer_subcommands` [INFO] [stdout] --> src/cli.rs:7:36 [INFO] [stdout] | [INFO] [stdout] 7 | #[clap(global_setting(AppSettings::InferSubcommands))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::HelpExpected`: Replaced with `Command::help_expected` [INFO] [stdout] --> src/cli.rs:8:36 [INFO] [stdout] | [INFO] [stdout] 8 | #[clap(global_setting(AppSettings::HelpExpected))] [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::SubcommandRequiredElseHelp`: Replaced with `Command::subcommand_required` combined with `Command::arg_required_else_help` [INFO] [stdout] --> src/cli.rs:9:29 [INFO] [stdout] | [INFO] [stdout] 9 | #[clap(setting(AppSettings::SubcommandRequiredElseHelp))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 37.01s [INFO] running `Command { std: "docker" "inspect" "895ce35213b877cb59bb70bb500653480225f91899b5c7363f71d578fd6a6b03", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "895ce35213b877cb59bb70bb500653480225f91899b5c7363f71d578fd6a6b03", kill_on_drop: false }` [INFO] [stdout] 895ce35213b877cb59bb70bb500653480225f91899b5c7363f71d578fd6a6b03 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/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=warn" "-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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] fa327301f9b663e06c8f35028fae863a74c60a2fc02cf8e0010d0bba4d153195 [INFO] running `Command { std: "docker" "start" "-a" "fa327301f9b663e06c8f35028fae863a74c60a2fc02cf8e0010d0bba4d153195", kill_on_drop: false }` [INFO] [stderr] warning: file found to be present in multiple build targets: /opt/rustwide/workdir/src/main.rs [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] [stdout] warning: use of deprecated variant `clap::AppSettings::PropagateVersion`: Replaced with `Command::propagate_version` and `Command::is_propagate_version_set` [INFO] [stdout] --> src/cli.rs:5:36 [INFO] [stdout] | [INFO] [stdout] 5 | #[clap(global_setting(AppSettings::PropagateVersion))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::InferSubcommands`: Replaced with `Command::infer_subcommands` [INFO] [stdout] --> src/cli.rs:7:36 [INFO] [stdout] | [INFO] [stdout] 7 | #[clap(global_setting(AppSettings::InferSubcommands))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::HelpExpected`: Replaced with `Command::help_expected` [INFO] [stdout] --> src/cli.rs:8:36 [INFO] [stdout] | [INFO] [stdout] 8 | #[clap(global_setting(AppSettings::HelpExpected))] [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::SubcommandRequiredElseHelp`: Replaced with `Command::subcommand_required` combined with `Command::arg_required_else_help` [INFO] [stdout] --> src/cli.rs:9:29 [INFO] [stdout] | [INFO] [stdout] 9 | #[clap(setting(AppSettings::SubcommandRequiredElseHelp))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::PropagateVersion`: Replaced with `Command::propagate_version` and `Command::is_propagate_version_set` [INFO] [stdout] --> src/cli.rs:5:36 [INFO] [stdout] | [INFO] [stdout] 5 | #[clap(global_setting(AppSettings::PropagateVersion))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::InferSubcommands`: Replaced with `Command::infer_subcommands` [INFO] [stdout] --> src/cli.rs:7:36 [INFO] [stdout] | [INFO] [stdout] 7 | #[clap(global_setting(AppSettings::InferSubcommands))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::HelpExpected`: Replaced with `Command::help_expected` [INFO] [stdout] --> src/cli.rs:8:36 [INFO] [stdout] | [INFO] [stdout] 8 | #[clap(global_setting(AppSettings::HelpExpected))] [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling rustybam v0.1.29 (/opt/rustwide/workdir) [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::SubcommandRequiredElseHelp`: Replaced with `Command::subcommand_required` combined with `Command::arg_required_else_help` [INFO] [stdout] --> src/cli.rs:9:29 [INFO] [stdout] | [INFO] [stdout] 9 | #[clap(setting(AppSettings::SubcommandRequiredElseHelp))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::PropagateVersion`: Replaced with `Command::propagate_version` and `Command::is_propagate_version_set` [INFO] [stdout] --> src/cli.rs:5:36 [INFO] [stdout] | [INFO] [stdout] 5 | #[clap(global_setting(AppSettings::PropagateVersion))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(deprecated)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::InferSubcommands`: Replaced with `Command::infer_subcommands` [INFO] [stdout] --> src/cli.rs:7:36 [INFO] [stdout] | [INFO] [stdout] 7 | #[clap(global_setting(AppSettings::InferSubcommands))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::HelpExpected`: Replaced with `Command::help_expected` [INFO] [stdout] --> src/cli.rs:8:36 [INFO] [stdout] | [INFO] [stdout] 8 | #[clap(global_setting(AppSettings::HelpExpected))] [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: use of deprecated variant `clap::AppSettings::SubcommandRequiredElseHelp`: Replaced with `Command::subcommand_required` combined with `Command::arg_required_else_help` [INFO] [stdout] --> src/cli.rs:9:29 [INFO] [stdout] | [INFO] [stdout] 9 | #[clap(setting(AppSettings::SubcommandRequiredElseHelp))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 4.68s [INFO] running `Command { std: "docker" "inspect" "fa327301f9b663e06c8f35028fae863a74c60a2fc02cf8e0010d0bba4d153195", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "fa327301f9b663e06c8f35028fae863a74c60a2fc02cf8e0010d0bba4d153195", kill_on_drop: false }` [INFO] [stdout] fa327301f9b663e06c8f35028fae863a74c60a2fc02cf8e0010d0bba4d153195 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/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=warn" "-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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 5066d024f44279746c289338bc1218203d612a8732841a988b15cbaeb172da30 [INFO] running `Command { std: "docker" "start" "-a" "5066d024f44279746c289338bc1218203d612a8732841a988b15cbaeb172da30", kill_on_drop: false }` [INFO] [stderr] warning: file found to be present in multiple build targets: /opt/rustwide/workdir/src/main.rs [INFO] [stderr] warning: use of deprecated variant `clap::AppSettings::PropagateVersion`: Replaced with `Command::propagate_version` and `Command::is_propagate_version_set` [INFO] [stderr] --> src/cli.rs:5:36 [INFO] [stderr] | [INFO] [stderr] 5 | #[clap(global_setting(AppSettings::PropagateVersion))] [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(deprecated)]` on by default [INFO] [stderr] [INFO] [stderr] warning: use of deprecated variant `clap::AppSettings::InferSubcommands`: Replaced with `Command::infer_subcommands` [INFO] [stderr] --> src/cli.rs:7:36 [INFO] [stderr] | [INFO] [stderr] 7 | #[clap(global_setting(AppSettings::InferSubcommands))] [INFO] [stderr] | ^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated variant `clap::AppSettings::HelpExpected`: Replaced with `Command::help_expected` [INFO] [stderr] --> src/cli.rs:8:36 [INFO] [stderr] | [INFO] [stderr] 8 | #[clap(global_setting(AppSettings::HelpExpected))] [INFO] [stderr] | ^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: use of deprecated variant `clap::AppSettings::SubcommandRequiredElseHelp`: Replaced with `Command::subcommand_required` combined with `Command::arg_required_else_help` [INFO] [stderr] --> src/cli.rs:9:29 [INFO] [stderr] | [INFO] [stderr] 9 | #[clap(setting(AppSettings::SubcommandRequiredElseHelp))] [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `rustybam` (build script) generated 4 warnings [INFO] [stderr] warning: `rustybam` (lib) generated 4 warnings (4 duplicates) [INFO] [stderr] warning: `rustybam` (lib test) generated 4 warnings (4 duplicates) [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 0.23s [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/rustybam-96d8e60856f6cb8a) [INFO] [stdout] [INFO] [stdout] running 8 tests [INFO] [stdout] test annotate::tests::test_chrom_specific_overlaps ... ok [INFO] [stdout] test bamstats::tests::test_add_cigar_stats ... ok [INFO] [stdout] test liftover::tests::check_invertible ... ok [INFO] [stdout] test suns::tests::test_convert ... ok [INFO] [stdout] test suns::tests::test_sun_finding ... ok [INFO] [stdout] test liftover::tests::test_aln_pair_liftover ... ok [INFO] [stdout] test trim_overlap::tests::test_inversion_trimming ... ok [INFO] [stdout] test bamstats::tests::test_cigar_stats_from_test_file ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 8 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.04s [INFO] [stdout] [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/rb-9dae8c0f8c946564) [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/rustybam-84307d3bd2d75fac) [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Doc-tests rustybam [INFO] [stdout] [INFO] [stdout] running 26 tests [INFO] [stdout] test src/suns.rs - suns::Genome::convert_from_idx (line 144) ... FAILED [INFO] [stderr] error: test failed, to rerun pass '--doc' [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `rustdoc --edition=2021 --crate-type lib --crate-name rustybam --test /opt/rustwide/workdir/src/lib.rs -L dependency=/opt/rustwide/target/debug/deps -L dependency=/opt/rustwide/target/debug/deps -L native=/opt/rustwide/target/debug/build/bzip2-sys-d433ac333b046c79/out/lib -L native=/opt/rustwide/target/debug/build/curl-sys-31cdd853c56d388b/out/build -L native=/opt/rustwide/target/debug/build/hts-sys-1a197d809a7d60d0/out -L native=/opt/rustwide/target/debug/build/libdeflate-sys-295e2656fa4a1334/out/lib -L native=/opt/rustwide/target/debug/build/libz-sys-2768172cd87d4a20/out/lib -L native=/opt/rustwide/target/debug/build/lzma-sys-8ea11a991f6e5270/out -L native=/opt/rustwide/target/debug/build/openssl-sys-4ccbbd8a24f5a6fc/out/openssl-build/install/lib --extern anyhow=/opt/rustwide/target/debug/deps/libanyhow-2d9de639ab954a37.rlib --extern bimap=/opt/rustwide/target/debug/deps/libbimap-0c6e5212acd7d098.rlib --extern bio=/opt/rustwide/target/debug/deps/libbio-1b03247b0341fe45.rlib --extern bio_types=/opt/rustwide/target/debug/deps/libbio_types-8fc537c9c8fc433a.rlib --extern calm_io=/opt/rustwide/target/debug/deps/libcalm_io-222a5ddaba87e756.rlib --extern chrono=/opt/rustwide/target/debug/deps/libchrono-d4f08e2e521be10c.rlib --extern clap=/opt/rustwide/target/debug/deps/libclap-3a77b243e7665e19.rlib --extern colored=/opt/rustwide/target/debug/deps/libcolored-98ea5425d3dd6da7.rlib --extern env_logger=/opt/rustwide/target/debug/deps/libenv_logger-b5a5b60dbb4dc54f.rlib --extern flate2=/opt/rustwide/target/debug/deps/libflate2-34960630b9bcbaf6.rlib --extern gzp=/opt/rustwide/target/debug/deps/libgzp-1fd443b97e053f57.rlib --extern itertools=/opt/rustwide/target/debug/deps/libitertools-1f40b5ee2082b85b.rlib --extern lazy_static=/opt/rustwide/target/debug/deps/liblazy_static-b341606102c7008f.rlib --extern log=/opt/rustwide/target/debug/deps/liblog-82c0db7e24d48d9b.rlib --extern natord=/opt/rustwide/target/debug/deps/libnatord-3524feb9f9359d71.rlib --extern needletail=/opt/rustwide/target/debug/deps/libneedletail-d65727f0a7a40391.rlib --extern rayon=/opt/rustwide/target/debug/deps/librayon-57780af13b81bf93.rlib --extern regex=/opt/rustwide/target/debug/deps/libregex-17f271d2d4d7a3b5.rlib --extern rust_htslib=/opt/rustwide/target/debug/deps/librust_htslib-d3380eee74579caf.rlib --extern rustybam=/opt/rustwide/target/debug/deps/librustybam-ac7ba36d8c021364.rlib -C embed-bitcode=no --cfg 'feature="any_zlib"' --cfg 'feature="default"' --cfg 'feature="deflate_zlib_ng"' --cfg 'feature="libdeflate"' --error-format human` (signal: 9, SIGKILL: kill) [INFO] running `Command { std: "docker" "inspect" "5066d024f44279746c289338bc1218203d612a8732841a988b15cbaeb172da30", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5066d024f44279746c289338bc1218203d612a8732841a988b15cbaeb172da30", kill_on_drop: false }` [INFO] [stdout] 5066d024f44279746c289338bc1218203d612a8732841a988b15cbaeb172da30