[INFO] cloning repository https://github.com/stela2502/bam_tide [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/stela2502/bam_tide" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_tide", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_tide'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] e64ac02708b743ad37ae0bcea3a25bb9bcc35fec [INFO] building stela2502/bam_tide against master#c7f6aa2869acdbf014d094c6e427e554e160b6db for pr-146237-2 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fbam_tide" "/workspace/builds/worker-7-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/stela2502/bam_tide [INFO] finished tweaking git repo https://github.com/stela2502/bam_tide [INFO] tweaked toml for git repo https://github.com/stela2502/bam_tide written to /workspace/builds/worker-7-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/stela2502/bam_tide on toolchain c7f6aa2869acdbf014d094c6e427e554e160b6db [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/stela2502/bam_tide 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" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Updating git repository `https://github.com/stela2502/cigar.git` [INFO] [stderr] Updating git repository `https://github.com/stela2502/int_to_str` [INFO] [stderr] Updating git repository `https://github.com/stela2502/mapping_info` [INFO] [stderr] Updating git repository `https://github.com/stela2502/scdata` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded attohttpc v0.25.0 [INFO] [stderr] Downloaded byteordered v0.6.0 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded index_list v0.2.16 [INFO] [stderr] Downloaded libdeflater v0.13.0 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded ufmt-macros v0.3.0 [INFO] [stderr] Downloaded ufmt-write v0.1.0 [INFO] [stderr] Downloaded libdeflate-sys v0.13.0 [INFO] [stderr] Downloaded ufmt v0.2.0 [INFO] [stderr] Downloaded rust-htslib v0.49.0 [INFO] [stderr] Downloaded curl-sys v0.4.82+curl-8.14.1 [INFO] [stderr] Downloaded hts-sys v2.2.0 [INFO] [stderr] Downloaded bigtools v0.5.6 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 8333c592f2296f0087eb07f32c7e956d9312ae16dd498abbc5ab2fad56088bb1 [INFO] running `Command { std: "docker" "start" "-a" "8333c592f2296f0087eb07f32c7e956d9312ae16dd498abbc5ab2fad56088bb1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "8333c592f2296f0087eb07f32c7e956d9312ae16dd498abbc5ab2fad56088bb1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8333c592f2296f0087eb07f32c7e956d9312ae16dd498abbc5ab2fad56088bb1", kill_on_drop: false }` [INFO] [stdout] 8333c592f2296f0087eb07f32c7e956d9312ae16dd498abbc5ab2fad56088bb1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 4436801f27549a48d68c74271682bb93ae695b580cc7b9de12c15145cc1d8c91 [INFO] running `Command { std: "docker" "start" "-a" "4436801f27549a48d68c74271682bb93ae695b580cc7b9de12c15145cc1d8c91", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.174 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling smallvec v1.15.1 [INFO] [stderr] Compiling memchr v2.7.5 [INFO] [stderr] Compiling libloading v0.8.8 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Compiling either v1.15.0 [INFO] [stderr] Compiling syn v2.0.104 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling portable-atomic v1.11.1 [INFO] [stderr] Compiling bitflags v2.9.1 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling percent-encoding v2.3.1 [INFO] [stderr] Compiling lazycell v1.3.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling futures-channel v0.3.31 [INFO] [stderr] Compiling regex v1.11.2 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Compiling form_urlencoded v1.2.1 [INFO] [stderr] Compiling anstyle-query v1.1.3 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling slab v0.4.10 [INFO] [stderr] Compiling unicode-width v0.2.1 [INFO] [stderr] Compiling anstream v0.6.19 [INFO] [stderr] Compiling byteorder v1.5.0 [INFO] [stderr] Compiling unit-prefix v0.5.1 [INFO] [stderr] Compiling chrono v0.4.41 [INFO] [stderr] Compiling num-format v0.4.4 [INFO] [stderr] Compiling rustls-native-certs v0.6.3 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling ufmt-macros v0.3.0 [INFO] [stderr] Compiling clap_builder v4.5.40 [INFO] [stderr] Compiling crc32fast v1.4.2 [INFO] [stderr] Compiling ufmt-write v0.1.0 [INFO] [stderr] Compiling byteordered v0.6.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling index_list v0.2.16 [INFO] [stderr] Compiling flate2 v1.1.2 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling int_to_str v0.1.0 (https://github.com/stela2502/int_to_str#c961fc73) [INFO] [stderr] Compiling cigar v0.1.0 (https://github.com/stela2502/cigar.git#5d434d47) [INFO] [stderr] Compiling ufmt v0.2.0 [INFO] [stderr] Compiling jobserver v0.1.33 [INFO] [stderr] Compiling getrandom v0.2.16 [INFO] [stderr] Compiling console v0.16.0 [INFO] [stderr] Compiling num_cpus v1.17.0 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling getrandom v0.3.3 [INFO] [stderr] Compiling dirs-sys v0.4.1 [INFO] [stderr] Compiling tempfile v3.22.0 [INFO] [stderr] Compiling directories v5.0.1 [INFO] [stderr] Compiling cc v1.2.29 [INFO] [stderr] Compiling indicatif v0.18.0 [INFO] [stderr] Compiling regex-automata v0.4.9 [INFO] [stderr] Compiling mapping_info v0.1.0 (https://github.com/stela2502/mapping_info#d5d2185e) [INFO] [stderr] Compiling scdata v0.1.0 (https://github.com/stela2502/scdata#85431205) [INFO] [stderr] Compiling openssl-src v300.5.1+3.5.1 [INFO] [stderr] Compiling cmake v0.1.54 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Compiling ring v0.17.14 [INFO] [stderr] Compiling curl-sys v0.4.82+curl-8.14.1 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Compiling libdeflate-sys v0.13.0 [INFO] [stderr] Compiling openssl-sys v0.9.109 [INFO] [stderr] Compiling libz-sys v1.1.22 [INFO] [stderr] Compiling synstructure v0.13.2 [INFO] [stderr] Compiling libdeflater v0.13.0 [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 futures-macro v0.3.31 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling serde_derive v1.0.219 [INFO] [stderr] Compiling thiserror-impl v2.0.12 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling tokio-macros v2.5.0 [INFO] [stderr] Compiling rustls v0.21.12 [INFO] [stderr] Compiling clap_derive v4.5.40 [INFO] [stderr] Compiling openssl-macros v0.1.1 [INFO] [stderr] Compiling derive-new v0.7.0 [INFO] [stderr] Compiling tokio v1.46.1 [INFO] [stderr] Compiling futures-util v0.3.31 [INFO] [stderr] Compiling zerofrom v0.1.6 [INFO] [stderr] Compiling yoke v0.8.0 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling thiserror v2.0.12 [INFO] [stderr] Compiling zerovec v0.11.2 [INFO] [stderr] Compiling zerotrie v0.2.2 [INFO] [stderr] Compiling bio-types v1.0.4 [INFO] [stderr] Compiling rustls-webpki v0.101.7 [INFO] [stderr] Compiling sct v0.7.1 [INFO] [stderr] Compiling webpki v0.22.4 [INFO] [stderr] Compiling clap v4.5.40 [INFO] [stderr] Compiling tinystr v0.8.1 [INFO] [stderr] Compiling potential_utf v0.1.2 [INFO] [stderr] Compiling serde v1.0.219 [INFO] [stderr] Compiling icu_collections v2.0.0 [INFO] [stderr] Compiling icu_locale_core v2.0.0 [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 hts-sys v2.2.0 [INFO] [stderr] Compiling futures-executor v0.3.31 [INFO] [stderr] Compiling futures v0.3.31 [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 attohttpc v0.25.0 [INFO] [stderr] Compiling bincode v1.3.3 [INFO] [stderr] Compiling bigtools v0.5.6 [INFO] [stderr] Compiling openssl v0.10.73 [INFO] [stderr] Compiling rust-htslib v0.49.0 [INFO] [stderr] Compiling bam_tide v0.4.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `scdata::scdata::MatrixValueType` [INFO] [stdout] --> src/mutation_processor.rs:18:5 [INFO] [stdout] | [INFO] [stdout] 18 | use scdata::scdata::MatrixValueType; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_mapping_quality` [INFO] [stdout] --> src/bed_data/bed_data.rs:259:73 [INFO] [stdout] | [INFO] [stdout] 259 | cell_tag: &[u8;2], umi_tag: &[u8;2], add_introns:bool, only_r1: bool, min_mapping_quality:u8 ) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_mapping_quality` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 4m 10s [INFO] running `Command { std: "docker" "inspect" "4436801f27549a48d68c74271682bb93ae695b580cc7b9de12c15145cc1d8c91", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "4436801f27549a48d68c74271682bb93ae695b580cc7b9de12c15145cc1d8c91", kill_on_drop: false }` [INFO] [stdout] 4436801f27549a48d68c74271682bb93ae695b580cc7b9de12c15145cc1d8c91 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-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" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] cd34ef008f7d4cfc95d004905ca1e1fad3c38d32795a574ffdd819c7dfaec3e1 [INFO] running `Command { std: "docker" "start" "-a" "cd34ef008f7d4cfc95d004905ca1e1fad3c38d32795a574ffdd819c7dfaec3e1", kill_on_drop: false }` [INFO] [stdout] warning: unused import: `scdata::scdata::MatrixValueType` [INFO] [stdout] --> src/mutation_processor.rs:18:5 [INFO] [stdout] | [INFO] [stdout] 18 | use scdata::scdata::MatrixValueType; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_mapping_quality` [INFO] [stdout] --> src/bed_data/bed_data.rs:259:73 [INFO] [stdout] | [INFO] [stdout] 259 | cell_tag: &[u8;2], umi_tag: &[u8;2], add_introns:bool, only_r1: bool, min_mapping_quality:u8 ) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_mapping_quality` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling bam_tide v0.4.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `std::process::exit` [INFO] [stdout] --> tests/test-bam2mut_hist.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::process::exit; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/bed_data/bed_data.rs:637:9 [INFO] [stdout] | [INFO] [stdout] 637 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::path::Path` [INFO] [stdout] --> src/bed_data/bed_data.rs:804:9 [INFO] [stdout] | [INFO] [stdout] 804 | use std::path::Path; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_mapping_quality` [INFO] [stdout] --> src/bed_data/bed_data.rs:259:73 [INFO] [stdout] | [INFO] [stdout] 259 | cell_tag: &[u8;2], umi_tag: &[u8;2], add_introns:bool, only_r1: bool, min_mapping_quality:u8 ) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_mapping_quality` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 8.09s [INFO] running `Command { std: "docker" "inspect" "cd34ef008f7d4cfc95d004905ca1e1fad3c38d32795a574ffdd819c7dfaec3e1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cd34ef008f7d4cfc95d004905ca1e1fad3c38d32795a574ffdd819c7dfaec3e1", kill_on_drop: false }` [INFO] [stdout] cd34ef008f7d4cfc95d004905ca1e1fad3c38d32795a574ffdd819c7dfaec3e1