[INFO] cloning repository https://github.com/kgori/pb_genotyper [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/kgori/pb_genotyper" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Fpb_genotyper", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Fpb_genotyper'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] d75384c05ee2c52725cc73fc3b717f492af69c01 [INFO] testing kgori/pb_genotyper against master#ad85bc524b1ad696e42061ad8338d382dffbdbe5 for pr-146237 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkgori%2Fpb_genotyper" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/kgori/pb_genotyper [INFO] finished tweaking git repo https://github.com/kgori/pb_genotyper [INFO] tweaked toml for git repo https://github.com/kgori/pb_genotyper written to /workspace/builds/worker-5-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/kgori/pb_genotyper on toolchain ad85bc524b1ad696e42061ad8338d382dffbdbe5 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/kgori/pb_genotyper 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" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded bio-types v1.0.1 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded nalgebra v0.29.0 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded multimap v0.9.1 [INFO] [stderr] Downloaded bio v1.6.0 [INFO] [stderr] Downloaded simba v0.6.0 [INFO] [stderr] Downloaded derive-new v0.5.9 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded wide v0.7.16 [INFO] [stderr] Downloaded rust-htslib v0.46.0 [INFO] [stderr] Downloaded statrs v0.16.0 [INFO] [stderr] Downloaded hts-sys v2.1.1 [INFO] [stderr] Downloaded libz-sys v1.1.16 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 02775a05fccb1554de7eac8aa2cc2689353cf75eb3e99eaf0321cfb659145a5f [INFO] running `Command { std: "docker" "start" "-a" "02775a05fccb1554de7eac8aa2cc2689353cf75eb3e99eaf0321cfb659145a5f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "02775a05fccb1554de7eac8aa2cc2689353cf75eb3e99eaf0321cfb659145a5f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "02775a05fccb1554de7eac8aa2cc2689353cf75eb3e99eaf0321cfb659145a5f", kill_on_drop: false }` [INFO] [stdout] 02775a05fccb1554de7eac8aa2cc2689353cf75eb3e99eaf0321cfb659145a5f [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] f3b66fbfdc0892d849877c1e9e4d8df0d97a8cdd9f71d560c748543685bad1bb [INFO] running `Command { std: "docker" "start" "-a" "f3b66fbfdc0892d849877c1e9e4d8df0d97a8cdd9f71d560c748543685bad1bb", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.153 [INFO] [stderr] Compiling proc-macro2 v1.0.81 [INFO] [stderr] Compiling autocfg v1.2.0 [INFO] [stderr] Compiling once_cell v1.19.0 [INFO] [stderr] Compiling memchr v2.7.2 [INFO] [stderr] Compiling serde v1.0.198 [INFO] [stderr] Compiling paste v1.0.14 [INFO] [stderr] Compiling bytemuck v1.15.0 [INFO] [stderr] Compiling rustversion v1.0.15 [INFO] [stderr] Compiling thiserror v1.0.59 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling anyhow v1.0.82 [INFO] [stderr] Compiling crc32fast v1.4.0 [INFO] [stderr] Compiling hashbrown v0.14.3 [INFO] [stderr] Compiling anstream v0.6.14 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling safe_arch v0.7.1 [INFO] [stderr] Compiling ryu v1.0.17 [INFO] [stderr] Compiling either v1.11.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling clap_lex v0.7.1 [INFO] [stderr] Compiling miniz_oxide v0.7.2 [INFO] [stderr] Compiling bit-set v0.5.3 [INFO] [stderr] Compiling itertools v0.11.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling num-traits v0.2.18 [INFO] [stderr] Compiling matrixmultiply v0.3.8 [INFO] [stderr] Compiling num-rational v0.4.1 [INFO] [stderr] Compiling wide v0.7.16 [INFO] [stderr] Compiling indexmap v2.2.6 [INFO] [stderr] Compiling clap_builder v4.5.7 [INFO] [stderr] Compiling strum v0.25.0 [INFO] [stderr] Compiling quote v1.0.36 [INFO] [stderr] Compiling syn v2.0.60 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling csv-core v0.1.11 [INFO] [stderr] Compiling editdistancek v1.0.2 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling bytecount v0.6.8 [INFO] [stderr] Compiling jobserver v0.1.31 [INFO] [stderr] Compiling getrandom v0.2.14 [INFO] [stderr] Compiling flate2 v1.0.28 [INFO] [stderr] Compiling petgraph v0.6.4 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling cc v1.0.95 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling regex-automata v0.4.6 [INFO] [stderr] Compiling num-integer v0.1.46 [INFO] [stderr] Compiling num-complex v0.4.5 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling ordered-float v3.9.2 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling cmake v0.1.50 [INFO] [stderr] Compiling simba v0.6.0 [INFO] [stderr] Compiling ndarray v0.15.6 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling hts-sys v2.1.1 [INFO] [stderr] Compiling libz-sys v1.1.16 [INFO] [stderr] Compiling regex v1.10.4 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling serde_derive v1.0.198 [INFO] [stderr] Compiling thiserror-impl v1.0.59 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling clap_derive v4.5.5 [INFO] [stderr] Compiling enum-map v2.7.3 [INFO] [stderr] Compiling bio-types v1.0.1 [INFO] [stderr] Compiling rust-htslib v0.46.0 [INFO] [stderr] Compiling clap v4.5.7 [INFO] [stderr] Compiling nalgebra v0.29.0 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling csv v1.3.0 [INFO] [stderr] Compiling multimap v0.9.1 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling statrs v0.16.0 [INFO] [stderr] Compiling bio v1.6.0 [INFO] [stderr] Compiling pb_genotyper v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 00s [INFO] running `Command { std: "docker" "inspect" "f3b66fbfdc0892d849877c1e9e4d8df0d97a8cdd9f71d560c748543685bad1bb", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f3b66fbfdc0892d849877c1e9e4d8df0d97a8cdd9f71d560c748543685bad1bb", kill_on_drop: false }` [INFO] [stdout] f3b66fbfdc0892d849877c1e9e4d8df0d97a8cdd9f71d560c748543685bad1bb [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] b830c0f3b5aef3623147aecbe4cbc889f042e55fbf49afc7de61b53601b8595d [INFO] running `Command { std: "docker" "start" "-a" "b830c0f3b5aef3623147aecbe4cbc889f042e55fbf49afc7de61b53601b8595d", kill_on_drop: false }` [INFO] [stderr] Compiling pb_genotyper v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 1.29s [INFO] running `Command { std: "docker" "inspect" "b830c0f3b5aef3623147aecbe4cbc889f042e55fbf49afc7de61b53601b8595d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b830c0f3b5aef3623147aecbe4cbc889f042e55fbf49afc7de61b53601b8595d", kill_on_drop: false }` [INFO] [stdout] b830c0f3b5aef3623147aecbe4cbc889f042e55fbf49afc7de61b53601b8595d [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+ad85bc524b1ad696e42061ad8338d382dffbdbe5" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] f56bfc56a7b423de82be575120b673ce881852aff61e1bbf4c40d17e79a4064c [INFO] running `Command { std: "docker" "start" "-a" "f56bfc56a7b423de82be575120b673ce881852aff61e1bbf4c40d17e79a4064c", kill_on_drop: false }` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.12s [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/pb_genotyper-e5dca00bc6e6e5e4) [INFO] [stdout] [INFO] [stdout] running 28 tests [INFO] [stdout] test cigar::tests::test_cigar_end_pos_refskip ... ok [INFO] [stdout] test cigar::tests::test_no_overlap_after_read ... ok [INFO] [stdout] test cigar::tests::test_cigar_end_pos_rnaseq ... ok [INFO] [stdout] test cigar::tests::test_no_overlap_rnaseq_split_read ... ok [INFO] [stdout] test cigar::tests::test_overlap_across_entire_read ... ok [INFO] [stdout] test cigar::tests::test_overlap_boundaries_single_match ... ok [INFO] [stdout] test cigar::tests::test_overlap_full_match ... ok [INFO] [stdout] test cigar::tests::test_no_overlap_before_read ... ok [INFO] [stdout] test cigar::tests::test_no_overlap_with_complex_cigar ... ok [INFO] [stdout] test cigar::tests::test_cigar_end_pos_simple ... ok [INFO] [stdout] test cigar::tests::test_overlap_rnaseq_read_pair ... ok [INFO] [stdout] test cigar::tests::test_overlap_with_insertion ... ok [INFO] [stdout] test cigar::tests::test_overlap_with_match_at_end ... ok [INFO] [stdout] test regions::tests::test_compress_regions_multiple_seqnames ... ok [INFO] [stdout] test regions::tests::test_compress_regions_non_overlapping ... ok [INFO] [stdout] test regions::tests::test_compress_regions_overlapping ... ok [INFO] [stdout] test regions::tests::test_convert_regions_vec_to_hashmap ... ok [INFO] [stdout] test cigar::tests::test_overlap_no_match ... ok [INFO] [stdout] test regions::tests::test_sort_regions_in_place_different_seqnames ... ok [INFO] [stdout] test regions::tests::test_sort_regions_in_place_same_seqname_different_starts ... ok [INFO] [stdout] test cigar::tests::test_overlap_partial_match ... ok [INFO] [stdout] test cigar::tests::test_overlap_with_match_at_start ... ok [INFO] [stdout] test cigar::tests::test_overlap_boundaries_region_match ... ok [INFO] [stdout] test cigar::tests::test_overlap_with_complex_cigar ... ok [INFO] [stdout] test cigar::tests::test_overlap_with_deletion ... ok [INFO] [stdout] test cigar::tests::test_overlap_rnaseq_split_read ... ok [INFO] [stdout] test cigar::tests::test_overlap_single_match_between_refskips ... ok [INFO] [stdout] test regions::tests::test_sort_regions_in_place_same_seqname_same_starts ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 28 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.21s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "f56bfc56a7b423de82be575120b673ce881852aff61e1bbf4c40d17e79a4064c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f56bfc56a7b423de82be575120b673ce881852aff61e1bbf4c40d17e79a4064c", kill_on_drop: false }` [INFO] [stdout] f56bfc56a7b423de82be575120b673ce881852aff61e1bbf4c40d17e79a4064c