[INFO] fetching crate sfs-cli 0.1.0... [INFO] testing sfs-cli-0.1.0 against try#8de4c7234dd9b97c9d76b58671343fdbbc9a433e+target=x86_64-unknown-linux-musl for musl_upgrade_1_2_5_with_libc_patch_0 [INFO] extracting crate sfs-cli 0.1.0 into /workspace/builds/worker-0-tc1/source [INFO] started tweaking crates.io crate sfs-cli 0.1.0 [INFO] finished tweaking crates.io crate sfs-cli 0.1.0 [INFO] tweaked toml for crates.io crate sfs-cli 0.1.0 written to /workspace/builds/worker-0-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate sfs-cli 0.1.0 on toolchain 8de4c7234dd9b97c9d76b58671343fdbbc9a433e [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate sfs-cli 0.1.0 already has a lockfile, it will not be regenerated [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded toml_datetime v0.6.3 [INFO] [stderr] Downloaded normalize-line-endings v0.3.0 [INFO] [stderr] Downloaded toml_edit v0.19.14 [INFO] [stderr] Downloaded serde_spanned v0.6.3 [INFO] [stderr] Downloaded serde_derive v1.0.188 [INFO] [stderr] Downloaded noodles-core v0.12.0 [INFO] [stderr] Downloaded trycmd v0.14.17 [INFO] [stderr] Downloaded percent-encoding v2.3.0 [INFO] [stderr] Downloaded snapbox-macros v0.3.5 [INFO] [stderr] Downloaded anstyle-wincon v2.1.0 [INFO] [stderr] Downloaded errno v0.3.2 [INFO] [stderr] Downloaded fastrand v2.0.0 [INFO] [stderr] Downloaded memoffset v0.9.0 [INFO] [stderr] Downloaded hermit-abi v0.3.2 [INFO] [stderr] Downloaded content_inspector v0.2.4 [INFO] [stderr] Downloaded noodles-tabix v0.26.0 [INFO] [stderr] Downloaded filetime v0.2.22 [INFO] [stderr] Downloaded clap_lex v0.5.1 [INFO] [stderr] Downloaded humantime-serde v1.1.1 [INFO] [stderr] Downloaded crossbeam-deque v0.8.3 [INFO] [stderr] Downloaded os_pipe v1.1.4 [INFO] [stderr] Downloaded tempfile v3.8.0 [INFO] [stderr] Downloaded dunce v1.0.4 [INFO] [stderr] Downloaded bitflags v2.4.0 [INFO] [stderr] Downloaded clap_derive v4.4.0 [INFO] [stderr] Downloaded env_logger v0.10.0 [INFO] [stderr] Downloaded sfs-core v0.1.0 [INFO] [stderr] Downloaded anyhow v1.0.75 [INFO] [stderr] Downloaded noodles-bcf v0.32.0 [INFO] [stderr] Downloaded clap v4.4.0 [INFO] [stderr] Downloaded flate2 v1.0.27 [INFO] [stderr] Downloaded noodles-vcf v0.35.0 [INFO] [stderr] Downloaded hashbrown v0.14.0 [INFO] [stderr] Downloaded winnow v0.5.15 [INFO] [stderr] Downloaded crossbeam-channel v0.5.8 [INFO] [stderr] Downloaded clap_builder v4.4.0 [INFO] [stderr] Downloaded rayon v1.7.0 [INFO] [stderr] Downloaded syn v2.0.29 [INFO] [stderr] Downloaded rayon-core v1.11.0 [INFO] [stderr] Downloaded memchr v2.6.0 [INFO] [stderr] Downloaded similar v2.2.1 [INFO] [stderr] Downloaded crossbeam-epoch v0.9.15 [INFO] [stderr] Downloaded serde v1.0.188 [INFO] [stderr] Downloaded indexmap v2.0.0 [INFO] [stderr] Downloaded noodles-bgzf v0.22.0 [INFO] [stderr] Downloaded rustix v0.38.9 [INFO] [stderr] Downloaded noodles-csi v0.22.0 [INFO] [stderr] Downloaded anstyle-parse v0.2.1 [INFO] [stderr] Downloaded anstyle v1.0.2 [INFO] [stderr] Downloaded once_cell v1.18.0 [INFO] [stderr] Downloaded crossbeam-utils v0.8.16 [INFO] [stderr] Downloaded proc-macro2 v1.0.66 [INFO] [stderr] Downloaded anstyle-query v1.0.0 [INFO] [stderr] Downloaded snapbox v0.4.12 [INFO] [stderr] Downloaded anstream v0.5.0 [INFO] [stderr] Downloaded unicode-ident v1.0.11 [INFO] [stderr] Downloaded libc v0.2.147 [INFO] [stderr] Downloaded linux-raw-sys v0.4.5 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 33f532f6f67772065e1af9c673d83394104bf7039311da378350542bf5a37d26 [INFO] running `Command { std: "docker" "start" "-a" "33f532f6f67772065e1af9c673d83394104bf7039311da378350542bf5a37d26", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "33f532f6f67772065e1af9c673d83394104bf7039311da378350542bf5a37d26", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "33f532f6f67772065e1af9c673d83394104bf7039311da378350542bf5a37d26", kill_on_drop: false }` [INFO] [stdout] 33f532f6f67772065e1af9c673d83394104bf7039311da378350542bf5a37d26 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/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" "RUSTDOCFLAGS=--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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "build" "--frozen" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] 4d0ac17b177a5d296625f0bae1502b3617678f86fdfce9d0c4da8327395eae03 [INFO] running `Command { std: "docker" "start" "-a" "4d0ac17b177a5d296625f0bae1502b3617678f86fdfce9d0c4da8327395eae03", kill_on_drop: false }` [INFO] [stderr] Compiling crossbeam-utils v0.8.16 [INFO] [stderr] Compiling crc32fast v1.3.2 [INFO] [stderr] Compiling adler v1.0.2 [INFO] [stderr] Compiling bytes v1.4.0 [INFO] [stderr] Compiling byteorder v1.4.3 [INFO] [stderr] Compiling hashbrown v0.14.0 [INFO] [stderr] Compiling proc-macro2 v1.0.66 [INFO] [stderr] Compiling unicode-ident v1.0.11 [INFO] [stderr] Compiling bit-vec v0.6.3 [INFO] [stderr] Compiling noodles-core v0.12.0 [INFO] [stderr] Compiling utf8parse v0.2.1 [INFO] [stderr] Compiling memchr v2.6.0 [INFO] [stderr] Compiling anstyle v1.0.2 [INFO] [stderr] Compiling percent-encoding v2.3.0 [INFO] [stderr] Compiling colorchoice v1.0.0 [INFO] [stderr] Compiling anstyle-query v1.0.0 [INFO] [stderr] Compiling miniz_oxide v0.7.1 [INFO] [stderr] Compiling anstyle-parse v0.2.1 [INFO] [stderr] Compiling clap_lex v0.5.1 [INFO] [stderr] Compiling strsim v0.10.0 [INFO] [stderr] Compiling heck v0.4.1 [INFO] [stderr] Compiling anyhow v1.0.75 [INFO] [stderr] Compiling once_cell v1.18.0 [INFO] [stderr] Compiling log v0.4.20 [INFO] [stderr] Compiling anstream v0.5.0 [INFO] [stderr] Compiling env_logger v0.10.0 [INFO] [stderr] Compiling clap_builder v4.4.0 [INFO] [stderr] Compiling flate2 v1.0.27 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling indexmap v2.0.0 [INFO] [stderr] Compiling crossbeam-channel v0.5.8 [INFO] [stderr] Compiling quote v1.0.33 [INFO] [stderr] Compiling noodles-bgzf v0.22.0 [INFO] [stderr] Compiling syn v2.0.29 [INFO] [stderr] Compiling noodles-csi v0.22.0 [INFO] [stderr] Compiling noodles-tabix v0.26.0 [INFO] [stderr] Compiling noodles-vcf v0.35.0 [INFO] [stderr] Compiling noodles-bcf v0.32.0 [INFO] [stderr] Compiling sfs-core v0.1.0 [INFO] [stderr] Compiling clap_derive v4.4.0 [INFO] [stderr] Compiling clap v4.4.0 [INFO] [stderr] Compiling sfs-cli v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 15.60s [INFO] running `Command { std: "docker" "inspect" "4d0ac17b177a5d296625f0bae1502b3617678f86fdfce9d0c4da8327395eae03", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "4d0ac17b177a5d296625f0bae1502b3617678f86fdfce9d0c4da8327395eae03", kill_on_drop: false }` [INFO] [stdout] 4d0ac17b177a5d296625f0bae1502b3617678f86fdfce9d0c4da8327395eae03 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/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" "RUSTDOCFLAGS=--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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "test" "--frozen" "--no-run" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] b6de31b6988bc2ee7fed75852eafeea7b33b482d8c3d55d997496607cd0073b1 [INFO] running `Command { std: "docker" "start" "-a" "b6de31b6988bc2ee7fed75852eafeea7b33b482d8c3d55d997496607cd0073b1", kill_on_drop: false }` [INFO] [stderr] Compiling crossbeam-utils v0.8.16 [INFO] [stderr] Compiling libc v0.2.147 [INFO] [stderr] Compiling autocfg v1.1.0 [INFO] [stderr] Compiling serde v1.0.188 [INFO] [stderr] Compiling rustix v0.38.9 [INFO] [stderr] Compiling linux-raw-sys v0.4.5 [INFO] [stderr] Compiling rayon-core v1.11.0 [INFO] [stderr] Compiling bitflags v2.4.0 [INFO] [stderr] Compiling same-file v1.0.6 [INFO] [stderr] Compiling fastrand v2.0.0 [INFO] [stderr] Compiling snapbox-macros v0.3.5 [INFO] [stderr] Compiling content_inspector v0.2.4 [INFO] [stderr] Compiling dunce v1.0.4 [INFO] [stderr] Compiling winnow v0.5.15 [INFO] [stderr] Compiling serde_derive v1.0.188 [INFO] [stderr] Compiling normalize-line-endings v0.3.0 [INFO] [stderr] Compiling similar v2.2.1 [INFO] [stderr] Compiling either v1.9.0 [INFO] [stderr] Compiling humantime v2.1.0 [INFO] [stderr] Compiling shlex v1.1.0 [INFO] [stderr] Compiling walkdir v2.3.3 [INFO] [stderr] Compiling glob v0.3.1 [INFO] [stderr] Compiling memoffset v0.9.0 [INFO] [stderr] Compiling crossbeam-epoch v0.9.15 [INFO] [stderr] Compiling crossbeam-channel v0.5.8 [INFO] [stderr] Compiling num_cpus v1.16.0 [INFO] [stderr] Compiling filetime v0.2.22 [INFO] [stderr] Compiling os_pipe v1.1.4 [INFO] [stderr] Compiling wait-timeout v0.2.0 [INFO] [stderr] Compiling crossbeam-deque v0.8.3 [INFO] [stderr] Compiling noodles-bgzf v0.22.0 [INFO] [stderr] Compiling noodles-csi v0.22.0 [INFO] [stderr] Compiling rayon v1.7.0 [INFO] [stderr] Compiling noodles-tabix v0.26.0 [INFO] [stderr] Compiling tempfile v3.8.0 [INFO] [stderr] Compiling noodles-vcf v0.35.0 [INFO] [stderr] Compiling snapbox v0.4.12 [INFO] [stderr] Compiling noodles-bcf v0.32.0 [INFO] [stderr] Compiling sfs-core v0.1.0 [INFO] [stderr] Compiling toml_datetime v0.6.3 [INFO] [stderr] Compiling serde_spanned v0.6.3 [INFO] [stderr] Compiling humantime-serde v1.1.1 [INFO] [stderr] Compiling toml_edit v0.19.14 [INFO] [stderr] Compiling sfs-cli v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Compiling trycmd v0.14.17 [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 18.82s [INFO] running `Command { std: "docker" "inspect" "b6de31b6988bc2ee7fed75852eafeea7b33b482d8c3d55d997496607cd0073b1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b6de31b6988bc2ee7fed75852eafeea7b33b482d8c3d55d997496607cd0073b1", kill_on_drop: false }` [INFO] [stdout] b6de31b6988bc2ee7fed75852eafeea7b33b482d8c3d55d997496607cd0073b1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/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" "RUSTDOCFLAGS=--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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "test" "--frozen" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] b61a89ea829c2c35aa09c31dae3d4f70a550dcda145d0e51f449231045d070b8 [INFO] running `Command { std: "docker" "start" "-a" "b61a89ea829c2c35aa09c31dae3d4f70a550dcda145d0e51f449231045d070b8", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.16s [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/sfs-1ddf6d11a9964828) [INFO] [stdout] [INFO] [stdout] running 7 tests [INFO] [stdout] test view::tests::test_marginalize_keep_and_remove_conflict ... ok [INFO] [stdout] test tests::test_no_subcommand ... ok [INFO] [stdout] test create::tests::test_project ... ok [INFO] [stdout] test create::tests::test_project_strict_conflict ... ok [INFO] [stdout] test create::tests::test_parse_samples ... ok [INFO] [stdout] test create::tests::test_project_args_conflict ... ok [INFO] [stdout] test create::tests::test_samples_and_samples_file_conflict ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s [INFO] [stdout] [INFO] [stderr] Running tests/cli_tests.rs (/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/cli_tests-0c2f8715837a3d8d) [INFO] [stdout] [INFO] [stdout] running 4 tests [INFO] [stderr] Testing tests/view/marginalize_from_npy.toml ... ok [INFO] [stderr] Testing tests/stat/f2_and_fst.toml ... ok [INFO] [stderr] Testing tests/create/missing_1d_all.toml ... ok [INFO] [stderr] Testing tests/fold/fold.toml ... ok [INFO] [stderr] Testing tests/view/marginalize_project.toml ... ok [INFO] [stderr] Testing tests/stat/invalid_precision.toml ... ok [INFO] [stderr] Testing tests/view/convert_to_npy.toml ... ok [INFO] [stderr] Testing tests/create/simple_vcf_gz_2d_subset.toml ... ok [INFO] [stderr] Testing tests/fold/fold_from_npy_inf.toml ... ok [INFO] [stderr] Testing tests/create/missing_1d_single.toml ... ok [INFO] [stderr] Testing tests/view/marginalize_keep_unordered.toml ... ok [INFO] [stderr] Testing tests/create/empty.toml ... ok [INFO] [stderr] Testing tests/create/simple_2d_subset.toml ... ok [INFO] [stderr] Testing tests/create/missing_1d_project_individuals.toml ... ok [INFO] [stderr] Testing tests/stat/relatedness.toml ... ok [INFO] [stderr] Testing tests/view/marginalize_remove.toml ... ok [INFO] [stderr] Testing tests/stat/heterozygosity.toml ... ok [INFO] [stderr] Testing tests/stat/precision.toml ... ok [INFO] [stderr] Testing tests/create/missing_1d_dimension_error_project.toml ... ok [INFO] [stderr] Testing tests/create/simple_vcf_1d_subset.toml ... ok [INFO] [stderr] Testing tests/create/simple_1d_all.toml ... ok [INFO] [stderr] Testing tests/create/missing_1d_invalid_project.toml ... ok [INFO] [stdout] test stat ... ok [INFO] [stderr] Testing tests/create/missing_3d_subset.toml ... ok [INFO] [stderr] Testing tests/create/missing_2d_project_subset.toml ... ok [INFO] [stderr] Testing tests/create/unknown.toml ... ok [INFO] [stderr] Testing tests/create/missing_1d_project.toml ... ok [INFO] [stdout] test view ... ok [INFO] [stderr] Testing tests/create/simple_2d_all.toml ... ok [INFO] [stdout] test fold ... ok [INFO] [stderr] Testing tests/create/large_4d_project_subset.toml ... ok [INFO] [stdout] test create ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 4 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.13s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "b61a89ea829c2c35aa09c31dae3d4f70a550dcda145d0e51f449231045d070b8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b61a89ea829c2c35aa09c31dae3d4f70a550dcda145d0e51f449231045d070b8", kill_on_drop: false }` [INFO] [stdout] b61a89ea829c2c35aa09c31dae3d4f70a550dcda145d0e51f449231045d070b8