[INFO] fetching crate rustybam 0.1.33... [INFO] testing rustybam-0.1.33 against try#f23b22458132fb20faeb8a915b1c252478696f25 for pr-131095 [INFO] extracting crate rustybam 0.1.33 into /workspace/builds/worker-7-tc2/source [INFO] validating manifest of crates.io crate rustybam 0.1.33 on toolchain f23b22458132fb20faeb8a915b1c252478696f25 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f23b22458132fb20faeb8a915b1c252478696f25" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] removed /workspace/builds/worker-7-tc2/source/.cargo/config [INFO] started tweaking crates.io crate rustybam 0.1.33 [INFO] finished tweaking crates.io crate rustybam 0.1.33 [INFO] tweaked toml for crates.io crate rustybam 0.1.33 written to /workspace/builds/worker-7-tc2/source/Cargo.toml [INFO] crate crates.io crate rustybam 0.1.33 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" "+f23b22458132fb20faeb8a915b1c252478696f25" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] warning: file `/workspace/builds/worker-7-tc2/source/src/main.rs` found to be present in multiple build targets: [INFO] [stderr] * `bin` target `rb` [INFO] [stderr] * `bin` target `rustybam` [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@sha256:6252d7ea7fb8caaf7af6d800c5fb250a9cd862b9a7f9508afb3c54fa7fe1102e" "/opt/rustwide/cargo-home/bin/cargo" "+f23b22458132fb20faeb8a915b1c252478696f25" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 655a3f2c1ac92b6dd6b5bba28c9cc201cc956065df8acbc08e63accac708f4d1 [INFO] running `Command { std: "docker" "start" "-a" "655a3f2c1ac92b6dd6b5bba28c9cc201cc956065df8acbc08e63accac708f4d1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "655a3f2c1ac92b6dd6b5bba28c9cc201cc956065df8acbc08e63accac708f4d1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "655a3f2c1ac92b6dd6b5bba28c9cc201cc956065df8acbc08e63accac708f4d1", kill_on_drop: false }` [INFO] [stdout] 655a3f2c1ac92b6dd6b5bba28c9cc201cc956065df8acbc08e63accac708f4d1 [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=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@sha256:6252d7ea7fb8caaf7af6d800c5fb250a9cd862b9a7f9508afb3c54fa7fe1102e" "/opt/rustwide/cargo-home/bin/cargo" "+f23b22458132fb20faeb8a915b1c252478696f25" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] c8f21f0d423b4ed56e705cac00d2a619a62594fc0c77d8d69736d343ad83a0d9 [INFO] running `Command { std: "docker" "start" "-a" "c8f21f0d423b4ed56e705cac00d2a619a62594fc0c77d8d69736d343ad83a0d9", kill_on_drop: false }` [INFO] [stderr] warning: file `/opt/rustwide/workdir/src/main.rs` found to be present in multiple build targets: [INFO] [stderr] * `bin` target `rb` [INFO] [stderr] * `bin` target `rustybam` [INFO] [stderr] Compiling proc-macro2 v1.0.63 [INFO] [stderr] Compiling unicode-ident v1.0.9 [INFO] [stderr] Compiling quote v1.0.29 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling libm v0.2.7 [INFO] [stderr] Compiling crossbeam-utils v0.8.16 [INFO] [stderr] Compiling rustversion v1.0.12 [INFO] [stderr] Compiling num-traits v0.2.15 [INFO] [stderr] Compiling num-integer v0.1.45 [INFO] [stderr] Compiling serde v1.0.164 [INFO] [stderr] Compiling memoffset v0.9.0 [INFO] [stderr] Compiling jobserver v0.1.26 [INFO] [stderr] Compiling getrandom v0.2.10 [INFO] [stderr] Compiling aho-corasick v1.0.2 [INFO] [stderr] Compiling matrixmultiply v0.3.7 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling paste v1.0.12 [INFO] [stderr] Compiling thiserror v1.0.40 [INFO] [stderr] Compiling ppv-lite86 v0.2.17 [INFO] [stderr] Compiling bytemuck v1.13.1 [INFO] [stderr] Compiling termcolor v1.2.0 [INFO] [stderr] Compiling cc v1.0.79 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling safe_arch v0.7.0 [INFO] [stderr] Compiling crossbeam-epoch v0.9.15 [INFO] [stderr] Compiling num-rational v0.4.1 [INFO] [stderr] Compiling regex-syntax v0.7.2 [INFO] [stderr] Compiling typenum v1.16.0 [INFO] [stderr] Compiling os_str_bytes v6.5.1 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling clap_lex v0.2.4 [INFO] [stderr] Compiling wide v0.7.10 [INFO] [stderr] Compiling num_cpus v1.16.0 [INFO] [stderr] Compiling either v1.8.1 [INFO] [stderr] Compiling cmake v0.1.50 [INFO] [stderr] Compiling openssl-src v111.26.0+1.1.1u [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling syn v2.0.22 [INFO] [stderr] Compiling textwrap v0.16.0 [INFO] [stderr] Compiling futures-core v0.3.28 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling log v0.4.19 [INFO] [stderr] Compiling strsim v0.10.0 [INFO] [stderr] Compiling humantime v2.1.0 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling libz-sys v1.1.9 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling openssl-sys v0.9.90 [INFO] [stderr] Compiling num-complex v0.4.3 [INFO] [stderr] Compiling curl-sys v0.4.63+curl-8.1.2 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling libdeflate-sys v0.12.0 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling hts-sys v2.1.1 [INFO] [stderr] Compiling lock_api v0.4.10 [INFO] [stderr] Compiling simba v0.6.0 [INFO] [stderr] Compiling snap v1.1.0 [INFO] [stderr] Compiling anyhow v1.0.71 [INFO] [stderr] Compiling rayon-core v1.11.0 [INFO] [stderr] Compiling regex v1.8.4 [INFO] [stderr] Compiling spin v0.9.8 [INFO] [stderr] Compiling crossbeam-deque v0.8.3 [INFO] [stderr] Compiling crossbeam-channel v0.5.8 [INFO] [stderr] Compiling nanorand v0.7.0 [INFO] [stderr] Compiling csv-core v0.1.10 [INFO] [stderr] Compiling ryu v1.0.13 [INFO] [stderr] Compiling fixedbitset v0.4.2 [INFO] [stderr] Compiling futures-sink v0.3.28 [INFO] [stderr] Compiling bit-vec v0.6.3 [INFO] [stderr] Compiling bytecount v0.6.3 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling itoa v1.0.6 [INFO] [stderr] Compiling petgraph v0.6.3 [INFO] [stderr] Compiling buffer-redux v1.0.0 [INFO] [stderr] Compiling bit-set v0.5.3 [INFO] [stderr] Compiling url v2.4.0 [INFO] [stderr] Compiling ndarray v0.15.6 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling ordered-float v3.7.0 [INFO] [stderr] Compiling itertools v0.11.0 [INFO] [stderr] Compiling core_affinity v0.8.0 [INFO] [stderr] Compiling env_logger v0.9.3 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling strum v0.25.0 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling editdistancek v1.0.2 [INFO] [stderr] Compiling chrono v0.4.26 [INFO] [stderr] Compiling rayon v1.7.0 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling itertools v0.10.5 [INFO] [stderr] Compiling colored v2.0.0 [INFO] [stderr] Compiling bimap v0.6.3 [INFO] [stderr] Compiling natord v1.0.9 [INFO] [stderr] Compiling clap_derive v3.2.25 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling strum_macros v0.24.3 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling libdeflater v0.12.0 [INFO] [stderr] Compiling calmio_filters v0.1.0 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Compiling enum-map v1.1.1 [INFO] [stderr] Compiling serde_derive v1.0.164 [INFO] [stderr] Compiling thiserror-impl v1.0.40 [INFO] [stderr] Compiling pin-project-internal v1.1.2 [INFO] [stderr] Compiling strum_macros v0.25.0 [INFO] [stderr] Compiling calm_io v0.1.1 [INFO] [stderr] Compiling bzip2 v0.4.4 [INFO] [stderr] Compiling nalgebra v0.29.0 [INFO] [stderr] Compiling bio-types v1.0.0 [INFO] [stderr] Compiling pin-project v1.1.2 [INFO] [stderr] Compiling flume v0.10.14 [INFO] [stderr] Compiling clap v3.2.25 [INFO] [stderr] Compiling flate2 v1.0.26 [INFO] [stderr] Compiling clap_complete v3.2.5 [INFO] [stderr] Compiling xz2 v0.1.7 [INFO] [stderr] Compiling gzp v0.11.3 [INFO] [stderr] Compiling needletail v0.5.1 [INFO] [stderr] Compiling rustybam v0.1.33 (/opt/rustwide/workdir) [INFO] [stderr] Compiling multimap v0.8.3 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling csv v1.2.2 [INFO] [stderr] Compiling statrs v0.16.0 [INFO] [stderr] Compiling bio v1.3.1 [INFO] [stderr] Compiling rust-htslib v0.44.1 [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 44.21s [INFO] running `Command { std: "docker" "inspect" "c8f21f0d423b4ed56e705cac00d2a619a62594fc0c77d8d69736d343ad83a0d9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "c8f21f0d423b4ed56e705cac00d2a619a62594fc0c77d8d69736d343ad83a0d9", kill_on_drop: false }` [INFO] [stdout] c8f21f0d423b4ed56e705cac00d2a619a62594fc0c77d8d69736d343ad83a0d9 [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=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@sha256:6252d7ea7fb8caaf7af6d800c5fb250a9cd862b9a7f9508afb3c54fa7fe1102e" "/opt/rustwide/cargo-home/bin/cargo" "+f23b22458132fb20faeb8a915b1c252478696f25" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 448fdb933bedc8c63479377a9f187841b308d30cadabe3ec846f3cc655b9bffa [INFO] running `Command { std: "docker" "start" "-a" "448fdb933bedc8c63479377a9f187841b308d30cadabe3ec846f3cc655b9bffa", kill_on_drop: false }` [INFO] [stderr] warning: file `/opt/rustwide/workdir/src/main.rs` found to be present in multiple build targets: [INFO] [stderr] * `bin` target `rb` [INFO] [stderr] * `bin` target `rustybam` [INFO] [stderr] Compiling rustybam v0.1.33 (/opt/rustwide/workdir) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 3.51s [INFO] running `Command { std: "docker" "inspect" "448fdb933bedc8c63479377a9f187841b308d30cadabe3ec846f3cc655b9bffa", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "448fdb933bedc8c63479377a9f187841b308d30cadabe3ec846f3cc655b9bffa", kill_on_drop: false }` [INFO] [stdout] 448fdb933bedc8c63479377a9f187841b308d30cadabe3ec846f3cc655b9bffa [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=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@sha256:6252d7ea7fb8caaf7af6d800c5fb250a9cd862b9a7f9508afb3c54fa7fe1102e" "/opt/rustwide/cargo-home/bin/cargo" "+f23b22458132fb20faeb8a915b1c252478696f25" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] eb43b76638d64e8cdf684dd078279c048e28a40f96a376a4608f2d9c443c1b17 [INFO] running `Command { std: "docker" "start" "-a" "eb43b76638d64e8cdf684dd078279c048e28a40f96a376a4608f2d9c443c1b17", kill_on_drop: false }` [INFO] [stderr] warning: file `/opt/rustwide/workdir/src/main.rs` found to be present in multiple build targets: [INFO] [stderr] * `bin` target `rb` [INFO] [stderr] * `bin` target `rustybam` [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.20s [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/rustybam-1db75369936d475a) [INFO] [stdout] [INFO] [stdout] running 8 tests [INFO] [stdout] test trim_overlap::tests::test_inversion_trimming ... ok [INFO] [stdout] test suns::tests::test_convert ... ok [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::test_aln_pair_liftover ... ok [INFO] [stdout] test suns::tests::test_sun_finding ... ok [INFO] [stdout] test liftover::tests::check_invertible ... 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 0.11s [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/rb-a313b3c1551438eb) [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/rustybam-07bd8e03bec26f4f) [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] [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/paf.rs - paf::PafRecord::get_target_as_region (line 471) ... ok [INFO] [stdout] test src/getfasta.rs - getfasta::get_fasta (line 12) ... ok [INFO] [stdout] test src/paf.rs - paf::PafRecord::new (line 373) ... ok [INFO] [stdout] test src/bed.rs - bed::parse_region (line 89) ... ok [INFO] [stdout] test src/liftover.rs - liftover::break_paf_on_indels (line 170) ... ok [INFO] [stdout] test src/bed.rs - bed::parse_bed (line 165) ... ok [INFO] [stdout] test src/paf.rs - paf::PafRecord::to_sam_string (line 862) ... ok [INFO] [stdout] test src/bed.rs - bed::parse_bed_rec (line 129) ... ok [INFO] [stdout] test src/paf.rs - paf::update_cigar_opt_len (line 979) ... ok [INFO] [stdout] test src/bed.rs - bed::has_overlap (line 49) ... ok [INFO] [stdout] test src/bed.rs - bed::split_region (line 196) ... ok [INFO] [stdout] test src/paf.rs - paf::consumes_query (line 954) ... ok [INFO] [stdout] test src/paf.rs - paf::cigar_from_str (line 1001) ... ok [INFO] [stdout] test src/nucfreq.rs - nucfreq::nucfreq (line 41) ... ok [INFO] [stdout] test src/paf.rs - paf::is_match (line 967) ... ok [INFO] [stdout] test src/suns.rs - suns::Genome::get_longest_perfect_repeats (line 85) ... ok [INFO] [stdout] test src/paf.rs - paf::cs_to_cigar (line 1104) ... ok [INFO] [stdout] test src/nucfreq.rs - nucfreq::region_nucfreq (line 99) ... ok [INFO] [stdout] test src/suns.rs - suns::Genome::get_shortest_subseq_size (line 62) ... ok [INFO] [stdout] test src/trim_overlap.rs - trim_overlap::trim_overlapping_pafs (line 22) ... ok [INFO] [stdout] test src/suns.rs - suns::Genome::from_file (line 50) ... ok [INFO] [stdout] test src/suns.rs - suns::Genome::convert_from_idx (line 144) ... ok [INFO] [stdout] test src/myio.rs - myio::reader (line 38) ... ok [INFO] [stdout] test src/fastx.rs - fastx::run_split_fastx (line 5) ... ok [INFO] [stdout] test src/paf.rs - paf::Paf::from_file (line 55) ... ok [INFO] [stdout] test src/paf.rs - paf::Paf::sam_header (line 310) ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 26 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 2.01s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "eb43b76638d64e8cdf684dd078279c048e28a40f96a376a4608f2d9c443c1b17", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "eb43b76638d64e8cdf684dd078279c048e28a40f96a376a4608f2d9c443c1b17", kill_on_drop: false }` [INFO] [stdout] eb43b76638d64e8cdf684dd078279c048e28a40f96a376a4608f2d9c443c1b17