[INFO] fetching crate sequintools 0.8.4... [INFO] testing sequintools-0.8.4 against try#b83b707f97d809763b7861afa7638871f3339a33 for pr-145838-1 [INFO] extracting crate sequintools 0.8.4 into /workspace/builds/worker-2-tc2/source [INFO] started tweaking crates.io crate sequintools 0.8.4 [INFO] finished tweaking crates.io crate sequintools 0.8.4 [INFO] tweaked toml for crates.io crate sequintools 0.8.4 written to /workspace/builds/worker-2-tc2/source/Cargo.toml [INFO] validating manifest of crates.io crate sequintools 0.8.4 on toolchain b83b707f97d809763b7861afa7638871f3339a33 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate sequintools 0.8.4 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" "+b83b707f97d809763b7861afa7638871f3339a33" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 36e7c8547fa359040bd73af173ecca126587780a0519012aea946ad7daebcada [INFO] running `Command { std: "docker" "start" "-a" "36e7c8547fa359040bd73af173ecca126587780a0519012aea946ad7daebcada", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "36e7c8547fa359040bd73af173ecca126587780a0519012aea946ad7daebcada", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "36e7c8547fa359040bd73af173ecca126587780a0519012aea946ad7daebcada", kill_on_drop: false }` [INFO] [stdout] 36e7c8547fa359040bd73af173ecca126587780a0519012aea946ad7daebcada [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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=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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] a6b80dc8b83b6a2edeb6e227374faff946a34e400720dc4012d58926cd5774cc [INFO] running `Command { std: "docker" "start" "-a" "a6b80dc8b83b6a2edeb6e227374faff946a34e400720dc4012d58926cd5774cc", kill_on_drop: false }` [INFO] [stderr] Compiling unicode-ident v1.0.11 [INFO] [stderr] Compiling pkg-config v0.3.27 [INFO] [stderr] Compiling memchr v2.5.0 [INFO] [stderr] Compiling regex-syntax v0.7.4 [INFO] [stderr] Compiling libc v0.2.169 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling libloading v0.8.5 [INFO] [stderr] Compiling either v1.13.0 [INFO] [stderr] Compiling zerocopy v0.8.14 [INFO] [stderr] Compiling bindgen v0.69.4 [INFO] [stderr] Compiling getrandom v0.3.1 [INFO] [stderr] Compiling bitflags v2.4.0 [INFO] [stderr] Compiling rustversion v1.0.14 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling proc-macro2 v1.0.89 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling thiserror v1.0.44 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling anstyle-parse v0.2.1 [INFO] [stderr] Compiling thiserror v2.0.3 [INFO] [stderr] Compiling percent-encoding v2.3.1 [INFO] [stderr] Compiling serde v1.0.185 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling anstream v0.6.18 [INFO] [stderr] Compiling form_urlencoded v1.2.1 [INFO] [stderr] Compiling quote v1.0.37 [INFO] [stderr] Compiling anyhow v1.0.98 [INFO] [stderr] Compiling clap_builder v4.5.41 [INFO] [stderr] Compiling syn v2.0.87 [INFO] [stderr] Compiling jobserver v0.1.32 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling ryu v1.0.18 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling itoa v1.0.11 [INFO] [stderr] Compiling byteorder v1.4.3 [INFO] [stderr] Compiling cc v1.1.18 [INFO] [stderr] Compiling aho-corasick v1.0.2 [INFO] [stderr] Compiling csv-core v0.1.11 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling regex-automata v0.3.3 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Compiling rand_core v0.9.0 [INFO] [stderr] Compiling openssl-src v111.26.0+1.1.1u [INFO] [stderr] Compiling cmake v0.1.50 [INFO] [stderr] Compiling rand_chacha v0.9.0 [INFO] [stderr] Compiling rand_pcg v0.9.0 [INFO] [stderr] Compiling openssl-sys v0.9.90 [INFO] [stderr] Compiling libz-sys v1.1.20 [INFO] [stderr] Compiling curl-sys v0.4.78+curl-8.11.0 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling rand v0.9.2 [INFO] [stderr] Compiling regex v1.9.1 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling strum_macros v0.24.3 [INFO] [stderr] Compiling csv v1.3.1 [INFO] [stderr] Compiling synstructure v0.13.2 [INFO] [stderr] Compiling zerofrom-derive v0.1.6 [INFO] [stderr] Compiling yoke-derive v0.8.0 [INFO] [stderr] Compiling zerovec-derive v0.11.1 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Compiling thiserror-impl v1.0.44 [INFO] [stderr] Compiling thiserror-impl v2.0.3 [INFO] [stderr] Compiling derive-new v0.7.0 [INFO] [stderr] Compiling clap_derive v4.5.41 [INFO] [stderr] Compiling zerofrom v0.1.6 [INFO] [stderr] Compiling bio-types v1.0.0 [INFO] [stderr] Compiling yoke v0.8.0 [INFO] [stderr] Compiling zerovec v0.11.2 [INFO] [stderr] Compiling zerotrie v0.2.2 [INFO] [stderr] Compiling clap v4.5.41 [INFO] [stderr] Compiling tinystr v0.8.1 [INFO] [stderr] Compiling potential_utf v0.1.2 [INFO] [stderr] Compiling icu_collections v2.0.0 [INFO] [stderr] Compiling icu_locale_core v2.0.0 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Compiling icu_provider v2.0.0 [INFO] [stderr] Compiling icu_normalizer v2.0.0 [INFO] [stderr] Compiling icu_properties v2.0.1 [INFO] [stderr] Compiling idna_adapter v1.2.1 [INFO] [stderr] Compiling idna v1.0.3 [INFO] [stderr] Compiling url v2.5.4 [INFO] [stderr] Compiling rust-htslib v0.50.0 [INFO] [stderr] Compiling sequintools v0.8.4 (/opt/rustwide/workdir) [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 28s [INFO] running `Command { std: "docker" "inspect" "a6b80dc8b83b6a2edeb6e227374faff946a34e400720dc4012d58926cd5774cc", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a6b80dc8b83b6a2edeb6e227374faff946a34e400720dc4012d58926cd5774cc", kill_on_drop: false }` [INFO] [stdout] a6b80dc8b83b6a2edeb6e227374faff946a34e400720dc4012d58926cd5774cc [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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=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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] f4a939661fdec8836c123f4b11f4742e92ca7efabf91217eb92c46c57fa7b67f [INFO] running `Command { std: "docker" "start" "-a" "f4a939661fdec8836c123f4b11f4742e92ca7efabf91217eb92c46c57fa7b67f", kill_on_drop: false }` [INFO] [stderr] Compiling rustix v1.0.1 [INFO] [stderr] Compiling bitflags v2.4.0 [INFO] [stderr] Compiling linux-raw-sys v0.9.2 [INFO] [stderr] Compiling once_cell v1.20.2 [INFO] [stderr] Compiling tempfile v3.20.0 [INFO] [stderr] Compiling sequintools v0.8.4 (/opt/rustwide/workdir) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 6.24s [INFO] running `Command { std: "docker" "inspect" "f4a939661fdec8836c123f4b11f4742e92ca7efabf91217eb92c46c57fa7b67f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f4a939661fdec8836c123f4b11f4742e92ca7efabf91217eb92c46c57fa7b67f", kill_on_drop: false }` [INFO] [stdout] f4a939661fdec8836c123f4b11f4742e92ca7efabf91217eb92c46c57fa7b67f [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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=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@sha256:7ad1b28ee6f5f7f699f6cf7015098d6ccdd96d6f2d78dd06228f5b4c9faf309c" "/opt/rustwide/cargo-home/bin/cargo" "+b83b707f97d809763b7861afa7638871f3339a33" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] c68d2cd534f7edf6a84b87b0b9253f335a849d7c02e5141319f523edcf70b00e [INFO] running `Command { std: "docker" "start" "-a" "c68d2cd534f7edf6a84b87b0b9253f335a849d7c02e5141319f523edcf70b00e", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.14s [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/sequintools-5a19767e5c418f38) [INFO] [stdout] [INFO] [stdout] running 51 tests [INFO] [stdout] test bedcov::tests::bedcov_with_wrong_bam_path ... ok [INFO] [stdout] test bedcov::tests::build_line ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_experimental_missing_sample_bed ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_by_standard_coverage_missing_bam ... ok [INFO] [stdout] test calibrate::tests::test_calibrated_error ... ok [INFO] [stdout] test calibrate::tests::test_choose_from ... ok [INFO] [stdout] test calibrate::tests::test_mean_depth ... ok [INFO] [stdout] chrom,beg,end,name,len,min,max,mean,std,cv [INFO] [stdout] chr1,99,199,region1,100,31,39,33.95,2.1650634,0.06377211 [INFO] [stdout] chr2,99,199,reg2,100,29,41,35.25,3.3087008,0.09386385 [INFO] [stdout] test calibrate::tests::test_mean_depth_chr2 ... ok [INFO] [stdout] test calibrate::tests::test_calibrated_contigs ... ok [INFO] [stdout] test bedcov::tests::bedcov_stdout ... ok [INFO] [stdout] test calibrate::tests::test_mean_depth_chr2_mapq10 ... ok [INFO] [stdout] chrom,beg,end,name,len,min,max,mean,std,cv [INFO] [stdout] chrQ_mirror,100,1000,decoy,900,0,0,0,0,NaN [INFO] [stdout] test bedcov::tests::bedcov_with_invalid_bed_path ... ok [INFO] [stdout] test bedcov::tests::bedcov_stdout_cram ... ok [INFO] [stdout] test calibrate::tests::test_subsample ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_regions ... ok [INFO] [stdout] test calibrate::tests::test_records_that_start_in_region ... ok [INFO] [stdout] test calibrate::tests::test_subsample_reject_read ... ok [INFO] [stdout] test calibrate::tests::test_window_starts ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_by_standard_coverage_cram ... ok [INFO] [stdout] test calibrate::tests::test_write_summary_report ... ok [INFO] [stdout] test calibrate::tests::test_write_summary_report_missing_output ... ok [INFO] [stdout] test calibrate::tests::test_window_starts_with_mapq ... ok [INFO] [stdout] test calibrate::tests::test_write_summary_report_with_sample ... ok [INFO] [stdout] test region::tests::display_region ... ok [INFO] [stdout] test region::tests::load_bed_to_vec ... ok [INFO] [stdout] test region::tests::load_invalid_reader ... ok [INFO] [stdout] test region::tests::load_multi_lines_bed ... ok [INFO] [stdout] test region::tests::load_with_bad_end ... ok [INFO] [stdout] test region::tests::load_with_bad_start ... ok [INFO] [stdout] test region::tests::load_without_name ... ok [INFO] [stdout] test tests::test_bedcov_command_parsing ... ok [INFO] [stdout] test tests::test_bedcov_short_command_parsing ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_by_sample_coverage_cram ... ok [INFO] [stdout] test tests::test_calibrate_command_parsing ... ok [INFO] [stdout] test calibrate::tests::test_write_summary_report_with_output ... ok [INFO] [stdout] test calibrate::tests::test_subsample_mate_before_read ... ok [INFO] [stdout] test tests::test_main_bedcov_execution ... ignored, TODO: add required mocks. [INFO] [stdout] test tests::test_main_calibrate_execution ... ignored, TODO: add required mocks. [INFO] [stdout] test tests::test_calibrate_short_command_parsing ... ok [INFO] [stdout] test calibrate::tests::test_subsample_read_in_hash ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_by_standard_coverage ... ok [INFO] [stdout] test calibrate::tests::test_calibrated_by_standard_coverage_cram_output ... ok [INFO] [stdout] test calibrate::tests::test_calibrate ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_by_standard_coverage_with_sample ... ok [INFO] [stdout] test bedcov::tests::bedcov_report_with_wtr ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_by_sample_coverage ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_by_sample_coverage_cram_output ... ok [INFO] [stdout] test calibrate::tests::test_calibrate_experimental ... ok [INFO] [stdout] test calibrate::tests::test_mean_depth_decreased_max_depth ... ok [INFO] [stdout] test calibrate::tests::test_mean_depth_max_depth_0 ... ok [INFO] [stdout] test calibrate::tests::test_mean_depth_increased_max_depth ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 49 passed; 0 failed; 2 ignored; 0 measured; 0 filtered out; finished in 0.77s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "c68d2cd534f7edf6a84b87b0b9253f335a849d7c02e5141319f523edcf70b00e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "c68d2cd534f7edf6a84b87b0b9253f335a849d7c02e5141319f523edcf70b00e", kill_on_drop: false }` [INFO] [stdout] c68d2cd534f7edf6a84b87b0b9253f335a849d7c02e5141319f523edcf70b00e