[INFO] cloning repository https://github.com/sharkLoc/bamkit
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/sharkLoc/bamkit" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FsharkLoc%2Fbamkit", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FsharkLoc%2Fbamkit'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 19d4533d17c2bb4f91d2c700283da3a2ad7b52ef
[INFO] checking sharkLoc/bamkit against master#3350c1eb3fd8fe1bee1ed4c76944d707bd256876 for pr-140558
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FsharkLoc%2Fbamkit" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/sharkLoc/bamkit on toolchain 3350c1eb3fd8fe1bee1ed4c76944d707bd256876
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+3350c1eb3fd8fe1bee1ed4c76944d707bd256876" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/sharkLoc/bamkit
[INFO] finished tweaking git repo https://github.com/sharkLoc/bamkit
[INFO] tweaked toml for git repo https://github.com/sharkLoc/bamkit written to /workspace/builds/worker-5-tc1/source/Cargo.toml
[INFO] crate git repo https://github.com/sharkLoc/bamkit 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" "+3350c1eb3fd8fe1bee1ed4c76944d707bd256876" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]      Locking 35 packages to latest compatible versions
[INFO] [stderr]       Adding anstream v0.6.18
[INFO] [stderr]       Adding anstyle v1.0.10
[INFO] [stderr]       Adding anstyle-parse v0.2.6
[INFO] [stderr]       Adding anstyle-query v1.1.2
[INFO] [stderr]       Adding anstyle-wincon v3.0.7
[INFO] [stderr]     Updating bitflags v1.3.2 -> v2.9.0
[INFO] [stderr]     Updating clap v4.0.26 -> v4.5.37
[INFO] [stderr]       Adding clap_builder v4.5.37
[INFO] [stderr]     Updating clap_derive v4.0.21 -> v4.5.32
[INFO] [stderr]     Updating clap_lex v0.3.0 -> v0.7.4
[INFO] [stderr]       Adding colorchoice v1.0.3
[INFO] [stderr]       Adding errno v0.3.11
[INFO] [stderr]       Adding heck v0.5.0
[INFO] [stderr]       Adding is_terminal_polyfill v1.70.1
[INFO] [stderr]     Updating libc v0.2.137 -> v0.2.172
[INFO] [stderr]       Adding linux-raw-sys v0.9.4
[INFO] [stderr]     Updating log v0.4.17 -> v0.4.27
[INFO] [stderr]     Updating once_cell v1.16.0 -> v1.21.3
[INFO] [stderr]     Updating proc-macro2 v1.0.47 -> v1.0.95
[INFO] [stderr]     Updating quote v1.0.21 -> v1.0.40
[INFO] [stderr]       Adding rustix v1.0.7
[INFO] [stderr]       Adding strsim v0.11.1
[INFO] [stderr]       Adding syn v2.0.101
[INFO] [stderr]       Adding terminal_size v0.4.2
[INFO] [stderr]       Adding utf8parse v0.2.2
[INFO] [stderr]       Adding windows-sys v0.59.0
[INFO] [stderr]       Adding windows-targets v0.52.6
[INFO] [stderr]       Adding windows_aarch64_gnullvm v0.52.6
[INFO] [stderr]       Adding windows_aarch64_msvc v0.52.6
[INFO] [stderr]       Adding windows_i686_gnu v0.52.6
[INFO] [stderr]       Adding windows_i686_gnullvm v0.52.6
[INFO] [stderr]       Adding windows_i686_msvc v0.52.6
[INFO] [stderr]       Adding windows_x86_64_gnu v0.52.6
[INFO] [stderr]       Adding windows_x86_64_gnullvm v0.52.6
[INFO] [stderr]       Adding windows_x86_64_msvc v0.52.6
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded plotly_derive v0.8.3
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded bio-types v0.13.0
[INFO] [stderr]   Downloaded rust-htslib v0.40.2
[INFO] [stderr]   Downloaded plotly v0.8.3
[INFO] [stderr]   Downloaded hts-sys v2.0.3
[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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+3350c1eb3fd8fe1bee1ed4c76944d707bd256876" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] a74ff4d9204607dbacf9d5ecb60909b64a8b138e30160576720c4ef8ed2477af
[INFO] running `Command { std: "docker" "start" "-a" "a74ff4d9204607dbacf9d5ecb60909b64a8b138e30160576720c4ef8ed2477af", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "a74ff4d9204607dbacf9d5ecb60909b64a8b138e30160576720c4ef8ed2477af", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a74ff4d9204607dbacf9d5ecb60909b64a8b138e30160576720c4ef8ed2477af", kill_on_drop: false }`
[INFO] [stdout] a74ff4d9204607dbacf9d5ecb60909b64a8b138e30160576720c4ef8ed2477af
[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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+3350c1eb3fd8fe1bee1ed4c76944d707bd256876" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 8c69d08e072157a5e40d50f58860c69ff61f4cbda20bd1ac229225fb3e70acfd
[INFO] running `Command { std: "docker" "start" "-a" "8c69d08e072157a5e40d50f58860c69ff61f4cbda20bd1ac229225fb3e70acfd", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.95
[INFO] [stderr]    Compiling libc v0.2.172
[INFO] [stderr]    Compiling unicode-ident v1.0.5
[INFO] [stderr]    Compiling syn v1.0.103
[INFO] [stderr]    Compiling pkg-config v0.3.26
[INFO] [stderr]    Compiling serde_derive v1.0.147
[INFO] [stderr]    Compiling autocfg v1.1.0
[INFO] [stderr]    Compiling version_check v0.9.4
[INFO] [stderr]    Compiling memchr v2.5.0
[INFO] [stderr]    Compiling serde v1.0.147
[INFO] [stderr]    Compiling serde_json v1.0.89
[INFO] [stderr]    Compiling unicase v2.6.0
[INFO] [stderr]    Compiling strsim v0.10.0
[INFO] [stderr]    Compiling ident_case v1.0.1
[INFO] [stderr]    Compiling fnv v1.0.7
[INFO] [stderr]     Checking percent-encoding v2.2.0
[INFO] [stderr]     Checking cfg-if v1.0.0
[INFO] [stderr]    Compiling quote v1.0.40
[INFO] [stderr]    Compiling num-traits v0.2.15
[INFO] [stderr]    Compiling mime_guess v2.0.4
[INFO] [stderr]    Compiling ryu v1.0.11
[INFO] [stderr]    Compiling minimal-lexical v0.2.1
[INFO] [stderr]    Compiling itoa v1.0.4
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling mime v0.3.16
[INFO] [stderr]    Compiling rustix v1.0.7
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking tinyvec_macros v0.1.0
[INFO] [stderr]    Compiling rustversion v1.0.9
[INFO] [stderr]     Checking tinyvec v1.6.0
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling nom v7.1.1
[INFO] [stderr]     Checking getrandom v0.2.8
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling jobserver v0.1.25
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]    Compiling cc v1.0.77
[INFO] [stderr]    Compiling glob v0.3.0
[INFO] [stderr]     Checking linux-raw-sys v0.9.4
[INFO] [stderr]    Compiling thiserror v1.0.37
[INFO] [stderr]     Checking bitflags v2.9.0
[INFO] [stderr]     Checking utf8parse v0.2.2
[INFO] [stderr]    Compiling askama_escape v0.10.3
[INFO] [stderr]    Compiling cmake v0.1.49
[INFO] [stderr]    Compiling openssl-src v111.24.0+1.1.1s
[INFO] [stderr]     Checking anstyle-parse v0.2.6
[INFO] [stderr]     Checking unicode-normalization v0.1.22
[INFO] [stderr]    Compiling libz-sys v1.1.8
[INFO] [stderr]    Compiling openssl-sys v0.9.77
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling curl-sys v0.4.59+curl-7.86.0
[INFO] [stderr]    Compiling hts-sys v2.0.3
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking aho-corasick v0.7.20
[INFO] [stderr]    Compiling erased-serde v0.3.23
[INFO] [stderr]     Checking anstyle-query v1.1.2
[INFO] [stderr]     Checking colorchoice v1.0.3
[INFO] [stderr]     Checking ppv-lite86 v0.2.17
[INFO] [stderr]    Compiling darling_core v0.14.2
[INFO] [stderr]    Compiling heck v0.4.0
[INFO] [stderr]     Checking lazy_static v1.4.0
[INFO] [stderr]     Checking unicode-bidi v0.3.8
[INFO] [stderr]     Checking humansize v1.1.1
[INFO] [stderr]     Checking anstyle v1.0.10
[INFO] [stderr]     Checking regex-syntax v0.6.28
[INFO] [stderr]     Checking is_terminal_polyfill v1.70.1
[INFO] [stderr]     Checking idna v0.3.0
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking anstream v0.6.18
[INFO] [stderr]     Checking terminal_size v0.4.2
[INFO] [stderr]    Compiling syn v2.0.101
[INFO] [stderr]     Checking form_urlencoded v1.1.0
[INFO] [stderr]     Checking clap_lex v0.7.4
[INFO] [stderr]    Compiling heck v0.5.0
[INFO] [stderr]     Checking strsim v0.11.1
[INFO] [stderr]     Checking clap_builder v4.5.37
[INFO] [stderr]     Checking url v2.3.1
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]     Checking regex v1.7.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]    Compiling thiserror-impl v1.0.37
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling strum_macros v0.24.3
[INFO] [stderr]    Compiling serde_repr v0.1.9
[INFO] [stderr]    Compiling darling_macro v0.14.2
[INFO] [stderr]     Checking once_cell v1.21.3
[INFO] [stderr]    Compiling darling v0.14.2
[INFO] [stderr]     Checking byteorder v1.4.3
[INFO] [stderr]    Compiling serde_with_macros v2.1.0
[INFO] [stderr]    Compiling plotly_derive v0.8.3
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking dyn-clone v1.0.9
[INFO] [stderr]     Checking colored v2.0.0
[INFO] [stderr]     Checking rand_pcg v0.3.1
[INFO] [stderr]     Checking log v0.4.27
[INFO] [stderr]     Checking bio-types v0.13.0
[INFO] [stderr]    Compiling clap_derive v4.5.32
[INFO] [stderr]     Checking clap v4.5.37
[INFO] [stderr]     Checking toml v0.5.9
[INFO] [stderr]     Checking serde_with v2.1.0
[INFO] [stderr]     Checking askama_shared v0.12.2
[INFO] [stderr]    Compiling askama_derive v0.11.2
[INFO] [stderr]     Checking askama v0.11.1
[INFO] [stderr]     Checking plotly v0.8.3
[INFO] [stderr]     Checking rust-htslib v0.40.2
[INFO] [stderr]     Checking bamkit v0.3.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 38s
[INFO] running `Command { std: "docker" "inspect" "8c69d08e072157a5e40d50f58860c69ff61f4cbda20bd1ac229225fb3e70acfd", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8c69d08e072157a5e40d50f58860c69ff61f4cbda20bd1ac229225fb3e70acfd", kill_on_drop: false }`
[INFO] [stdout] 8c69d08e072157a5e40d50f58860c69ff61f4cbda20bd1ac229225fb3e70acfd
