[INFO] cloning repository https://github.com/keithyin/gskits
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/keithyin/gskits" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Fgskits", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Fgskits'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] b30580e26b2a665cb4250808dab459980ce33b2c
[INFO] testing keithyin/gskits against beta-2025-09-21 for beta-1.91-3
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Fgskits" "/workspace/builds/worker-7-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/keithyin/gskits
[INFO] finished tweaking git repo https://github.com/keithyin/gskits
[INFO] tweaked toml for git repo https://github.com/keithyin/gskits written to /workspace/builds/worker-7-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/keithyin/gskits on toolchain beta-2025-09-21
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2025-09-21" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/keithyin/gskits 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" "+beta-2025-09-21" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] ae4a0d9bb97dc129583e352babd2302fe28d1f7aed400644f68867fe8081f5de
[INFO] running `Command { std: "docker" "start" "-a" "ae4a0d9bb97dc129583e352babd2302fe28d1f7aed400644f68867fe8081f5de", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "ae4a0d9bb97dc129583e352babd2302fe28d1f7aed400644f68867fe8081f5de", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ae4a0d9bb97dc129583e352babd2302fe28d1f7aed400644f68867fe8081f5de", kill_on_drop: false }`
[INFO] [stdout] ae4a0d9bb97dc129583e352babd2302fe28d1f7aed400644f68867fe8081f5de
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/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" "RUSTDOCFLAGS=--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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] d56ccb3acb81ad3d11caf19394c7cc528e0e790b9f98ebc856ac064ba33708ff
[INFO] running `Command { std: "docker" "start" "-a" "d56ccb3acb81ad3d11caf19394c7cc528e0e790b9f98ebc856ac064ba33708ff", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.94
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[INFO] [stderr]    Compiling editdistancek v1.0.2
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[INFO] [stderr]    Compiling linear-map v1.2.0
[INFO] [stderr]    Compiling sha1_smol v1.0.1
[INFO] [stderr]    Compiling triple_accel v0.4.0
[INFO] [stderr]    Compiling strum v0.26.3
[INFO] [stderr]    Compiling chrono v0.4.40
[INFO] [stderr]    Compiling simba v0.9.0
[INFO] [stderr]    Compiling uuid v1.16.0
[INFO] [stderr]    Compiling indicatif v0.17.11
[INFO] [stderr]    Compiling openssl-src v300.5.0+3.5.0
[INFO] [stderr]    Compiling cmake v0.1.54
[INFO] [stderr]    Compiling sysinfo v0.34.2
[INFO] [stderr]    Compiling num_cpus v1.16.0
[INFO] [stderr]    Compiling rand_distr v0.4.3
[INFO] [stderr]    Compiling openssl-sys v0.9.107
[INFO] [stderr]    Compiling libz-sys v1.1.22
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling curl-sys v0.4.80+curl-8.12.1
[INFO] [stderr]    Compiling synstructure v0.13.1
[INFO] [stderr]    Compiling zerofrom-derive v0.1.6
[INFO] [stderr]    Compiling yoke-derive v0.7.5
[INFO] [stderr]    Compiling zerovec-derive v0.10.3
[INFO] [stderr]    Compiling displaydoc v0.2.5
[INFO] [stderr]    Compiling icu_provider_macros v1.5.0
[INFO] [stderr]    Compiling serde_derive v1.0.219
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]    Compiling thiserror-impl v2.0.12
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling tracing-attributes v0.1.28
[INFO] [stderr]    Compiling derive-new v0.7.0
[INFO] [stderr]    Compiling enum-map v2.7.3
[INFO] [stderr]    Compiling zerofrom v0.1.6
[INFO] [stderr]    Compiling yoke v0.7.5
[INFO] [stderr]    Compiling thiserror v1.0.69
[INFO] [stderr]    Compiling zerovec v0.10.4
[INFO] [stderr]    Compiling tracing v0.1.41
[INFO] [stderr]    Compiling bio-types v1.0.4
[INFO] [stderr]    Compiling tinystr v0.7.6
[INFO] [stderr]    Compiling icu_collections v1.5.0
[INFO] [stderr]    Compiling icu_locid v1.5.0
[INFO] [stderr]    Compiling nalgebra v0.33.2
[INFO] [stderr]    Compiling icu_provider v1.5.0
[INFO] [stderr]    Compiling icu_locid_transform v1.5.0
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]    Compiling hts-sys v2.2.0
[INFO] [stderr]    Compiling icu_properties v1.5.1
[INFO] [stderr]    Compiling icu_normalizer v1.5.0
[INFO] [stderr]    Compiling csv v1.3.1
[INFO] [stderr]    Compiling multimap v0.10.0
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling idna_adapter v1.2.0
[INFO] [stderr]    Compiling idna v1.0.3
[INFO] [stderr]    Compiling url v2.5.4
[INFO] [stderr]    Compiling statrs v0.18.0
[INFO] [stderr]    Compiling bio v2.2.0
[INFO] [stderr]    Compiling rust-htslib v0.49.0
[INFO] [stderr]    Compiling gskits v0.15.15 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 05s
[INFO] running `Command { std: "docker" "inspect" "d56ccb3acb81ad3d11caf19394c7cc528e0e790b9f98ebc856ac064ba33708ff", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "d56ccb3acb81ad3d11caf19394c7cc528e0e790b9f98ebc856ac064ba33708ff", kill_on_drop: false }`
[INFO] [stdout] d56ccb3acb81ad3d11caf19394c7cc528e0e790b9f98ebc856ac064ba33708ff
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/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" "RUSTDOCFLAGS=--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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] cd2634e02bfbd64bd1dcfd458ba48248c461b3e26742d3b3ebdb2dfce6d7b246
[INFO] running `Command { std: "docker" "start" "-a" "cd2634e02bfbd64bd1dcfd458ba48248c461b3e26742d3b3ebdb2dfce6d7b246", kill_on_drop: false }`
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.18
[INFO] [stderr]    Compiling rayon-core v1.12.1
[INFO] [stderr]    Compiling serde_json v1.0.140
[INFO] [stderr]    Compiling unicode-width v0.1.14
[INFO] [stderr]    Compiling plotters-backend v0.3.7
[INFO] [stderr]    Compiling itertools v0.10.5
[INFO] [stderr]    Compiling half v1.8.3
[INFO] [stderr]    Compiling cast v0.3.0
[INFO] [stderr]    Compiling atty v0.2.14
[INFO] [stderr]    Compiling oorandom v11.1.5
[INFO] [stderr]    Compiling crossbeam-deque v0.8.6
[INFO] [stderr]    Compiling serde_cbor v0.11.2
[INFO] [stderr]    Compiling textwrap v0.11.0
[INFO] [stderr]    Compiling plotters-svg v0.3.7
[INFO] [stderr]    Compiling clap v2.34.0
[INFO] [stderr]    Compiling plotters v0.3.7
[INFO] [stderr]    Compiling rayon v1.10.0
[INFO] [stderr]    Compiling tinytemplate v1.2.1
[INFO] [stderr]    Compiling criterion-plot v0.4.5
[INFO] [stderr]    Compiling criterion v0.3.6
[INFO] [stderr]    Compiling gskits v0.15.15 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 18.70s
[INFO] running `Command { std: "docker" "inspect" "cd2634e02bfbd64bd1dcfd458ba48248c461b3e26742d3b3ebdb2dfce6d7b246", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "cd2634e02bfbd64bd1dcfd458ba48248c461b3e26742d3b3ebdb2dfce6d7b246", kill_on_drop: false }`
[INFO] [stdout] cd2634e02bfbd64bd1dcfd458ba48248c461b3e26742d3b3ebdb2dfce6d7b246
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc2/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" "RUSTDOCFLAGS=--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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 3b2fa6960933aedacf9bc9ba7fb31c393b96e43a2d4102f3657bcaf8660661ae
[INFO] running `Command { std: "docker" "start" "-a" "3b2fa6960933aedacf9bc9ba7fb31c393b96e43a2d4102f3657bcaf8660661ae", kill_on_drop: false }`
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.28s
[INFO] [stderr]      Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/gskits-0dce513e598e2153)
[INFO] [stdout] 
[INFO] [stdout] running 28 tests
[INFO] [stdout] test dna::test::test_bio_alpha ... ok
[INFO] [stdout] test gsbam::cigar_ext::tests::test_edge_cases ... ok
[INFO] [stdout] test ds::test::test_read_info ... ok
[INFO] [stdout] test gsbam::cigar_ext::tests::test_ideneity_special_case ... ok
[INFO] [stdout] test gsbam::cigar_ext::tests::test_parse_cigar_str ... ok
[INFO] [stdout] test ds::region::test::test_calcute_gaps ... ok
[INFO] [stdout] test ds::region::test::test_calcute_overlap_metrics ... ok
[INFO] [stdout] test gsbam::cigar_ext::tests::test_long_ins_regions_in_query ... ok
[INFO] [stdout] test dna::test::test_reverse_complement ... ok
[INFO] [stdout] test gsbam::cigar_ext::tests::test_range_identity ... ok
[INFO] [stdout] test gsbam::plp_counts_from_records::test::test_plp_cnts ... ok
[INFO] [stdout] test gsbam::plp_counts_from_records::test::test_region_plp_cnts ... ok
[INFO] [stdout] test gsbam::bam_header_ext::test::test_header_ext ... ok
[INFO] [stdout] test gsbam::bam_header_ext::test::test_rg_rn_mapping ... ok
[INFO] [stdout] test gsbam::plp_counts_from_records::test::test_test_plp_using_aligned_pairs_with_indel ... ok
[INFO] [stdout] test gsbam::plp_counts_from_records::test::test_test_plp_using_aligned_pairs_with_right_soft_clip ... ok
[INFO] [stdout] test matrix::transpose::test::test_transpose ... ok
[INFO] [stdout] test phreq::test::test_phreq2quality ... ok
[INFO] [stdout] test gsbam::plp_counts_from_records::test::test_plp_cnts_with_blacklist ... ok
[INFO] [stdout] test matrix::transpose::test::test_transpose_blocked ... ok
[INFO] [stdout] test phreq::test::test_phreq_list_2_err_list ... ok
[INFO] [stdout] test test::test_alphabet ... ok
[INFO] [stdout] test utils::test::test_range_parser ... ok
[INFO] [stdout] test poly_n::test::test_find_homopolymer_regions ... ok
[INFO] [stdout] test phreq::test::test_phreq_list_2_quality ... ok
[INFO] [stdout] test phreq::test::test_quality_2_phreq ... ok
[INFO] [stdout] test phreq::test::test_phreq_list_2_quality_list ... ok
[INFO] [stdout] test gsbam::plp_counts_from_records::test::test_plp_within_region ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 28 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.03s
[INFO] [stdout] 
[INFO] [stderr]    Doc-tests gskits
[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] running `Command { std: "docker" "inspect" "3b2fa6960933aedacf9bc9ba7fb31c393b96e43a2d4102f3657bcaf8660661ae", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "3b2fa6960933aedacf9bc9ba7fb31c393b96e43a2d4102f3657bcaf8660661ae", kill_on_drop: false }`
[INFO] [stdout] 3b2fa6960933aedacf9bc9ba7fb31c393b96e43a2d4102f3657bcaf8660661ae