[INFO] cloning repository https://github.com/keithyin/bam2ab1 [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/keithyin/bam2ab1" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Fbam2ab1", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Fbam2ab1'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 8f08dc451eee10557b895b8db57bb12ac7a2d2b1 [INFO] checking keithyin/bam2ab1/8f08dc451eee10557b895b8db57bb12ac7a2d2b1 against master#f5e2df741b4a9820a7579f0c8eccc951706a8782 for pr-147984 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Fbam2ab1" "/workspace/builds/worker-1-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-1-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/keithyin/bam2ab1 [INFO] finished tweaking git repo https://github.com/keithyin/bam2ab1 [INFO] tweaked toml for git repo https://github.com/keithyin/bam2ab1 written to /workspace/builds/worker-1-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/keithyin/bam2ab1 on toolchain f5e2df741b4a9820a7579f0c8eccc951706a8782 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f5e2df741b4a9820a7579f0c8eccc951706a8782" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/keithyin/bam2ab1 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" "+f5e2df741b4a9820a7579f0c8eccc951706a8782" "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] Downloading crates ... [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded cc v1.2.37 [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded ordered-float v5.0.0 [INFO] [stderr] Downloaded fixedbitset v0.5.7 [INFO] [stderr] Downloaded anstream v0.6.20 [INFO] [stderr] Downloaded clap_derive v4.5.47 [INFO] [stderr] Downloaded bincode v2.0.1 [INFO] [stderr] Downloaded clap v4.5.48 [INFO] [stderr] Downloaded safe_arch v0.7.4 [INFO] [stderr] Downloaded statrs v0.18.0 [INFO] [stderr] Downloaded wide v0.7.33 [INFO] [stderr] Downloaded clap_builder v4.5.48 [INFO] [stderr] Downloaded indexmap v2.11.3 [INFO] [stderr] Downloaded windows-core v0.57.0 [INFO] [stderr] Downloaded sysinfo v0.34.2 [INFO] [stderr] Downloaded bindgen v0.69.5 [INFO] [stderr] Downloaded toml_edit v0.23.5 [INFO] [stderr] Downloaded bio v2.3.0 [INFO] [stderr] Downloaded 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"/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" "+f5e2df741b4a9820a7579f0c8eccc951706a8782" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 18d5e4b3bd60c8e327547ef8da4edeac1116842b410a66d19674e5bb54734e9d [INFO] running `Command { std: "docker" "start" "-a" "18d5e4b3bd60c8e327547ef8da4edeac1116842b410a66d19674e5bb54734e9d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "18d5e4b3bd60c8e327547ef8da4edeac1116842b410a66d19674e5bb54734e9d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "18d5e4b3bd60c8e327547ef8da4edeac1116842b410a66d19674e5bb54734e9d", kill_on_drop: false }` [INFO] [stdout] 18d5e4b3bd60c8e327547ef8da4edeac1116842b410a66d19674e5bb54734e9d [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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" "+f5e2df741b4a9820a7579f0c8eccc951706a8782" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 9b504fac60add2a8ad54e2ee030fda6b53b3605bcaa73e84e201975fdc43dc03 [INFO] running `Command { std: "docker" "start" "-a" "9b504fac60add2a8ad54e2ee030fda6b53b3605bcaa73e84e201975fdc43dc03", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.101 [INFO] [stderr] Compiling unicode-ident v1.0.19 [INFO] [stderr] Compiling libc v0.2.175 [INFO] [stderr] Compiling find-msvc-tools v0.1.1 [INFO] [stderr] Compiling pkg-config v0.3.32 [INFO] [stderr] Compiling libm v0.2.15 [INFO] [stderr] Compiling serde_core v1.0.225 [INFO] [stderr] Checking memchr v2.7.5 [INFO] [stderr] Compiling zerocopy v0.8.27 [INFO] [stderr] Compiling glob v0.3.3 [INFO] [stderr] Compiling serde v1.0.225 [INFO] [stderr] Checking writeable v0.6.1 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Checking cfg-if v1.0.3 [INFO] [stderr] Compiling rustversion v1.0.22 [INFO] [stderr] Checking litemap v0.8.0 [INFO] [stderr] Compiling icu_properties_data v2.0.1 [INFO] [stderr] Compiling regex-syntax v0.8.6 [INFO] [stderr] Compiling icu_normalizer_data v2.0.0 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling libloading v0.8.8 [INFO] [stderr] Compiling matrixmultiply v0.3.10 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Compiling either v1.15.0 [INFO] [stderr] Checking bytemuck v1.23.2 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking safe_arch v0.7.4 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Compiling hashbrown v0.15.5 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v0.5.7 [INFO] [stderr] Checking unicode-width v0.2.1 [INFO] [stderr] Compiling virtue v0.0.18 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking itertools v0.14.0 [INFO] [stderr] Checking simba v0.9.1 [INFO] [stderr] Checking anstream v0.6.20 [INFO] [stderr] Checking rand v0.8.5 [INFO] [stderr] Compiling toml_edit v0.23.5 [INFO] [stderr] Checking console v0.15.11 [INFO] [stderr] Checking bit-set v0.8.0 [INFO] [stderr] Checking ndarray v0.16.1 [INFO] [stderr] Checking tracing-core v0.1.34 [INFO] [stderr] Compiling libz-sys v1.1.22 [INFO] [stderr] Compiling openssl-sys v0.9.109 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling curl-sys v0.4.83+curl-8.15.0 [INFO] [stderr] Compiling bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Compiling bincode_derive v2.0.1 [INFO] [stderr] Checking rand_distr v0.4.3 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Compiling regex v1.11.2 [INFO] [stderr] Compiling proc-macro-crate v3.4.0 [INFO] [stderr] 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v1.0.4 [INFO] [stderr] Checking clap v4.5.48 [INFO] [stderr] Checking nalgebra v0.33.2 [INFO] [stderr] Checking tinystr v0.8.1 [INFO] [stderr] Checking potential_utf v0.1.3 [INFO] [stderr] Checking icu_locale_core v2.0.0 [INFO] [stderr] Checking icu_collections v2.0.0 [INFO] [stderr] Checking icu_provider v2.0.0 [INFO] [stderr] Checking icu_normalizer v2.0.0 [INFO] [stderr] Checking icu_properties v2.0.1 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking multimap v0.10.1 [INFO] [stderr] Checking bv v0.11.1 [INFO] [stderr] Checking csv v1.3.1 [INFO] [stderr] Checking idna_adapter v1.2.1 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Checking idna v1.1.0 [INFO] [stderr] Checking url v2.5.7 [INFO] [stderr] Checking statrs v0.18.0 [INFO] [stderr] Checking bio v2.3.0 [INFO] [stderr] Checking rust-htslib v0.49.0 [INFO] [stderr] Checking gskits v0.15.15 [INFO] [stderr] Checking bam2ab1 v0.1.2 (/opt/rustwide/workdir) [INFO] [stdout] warning: unexpected `cfg` condition value: `encode` [INFO] [stdout] --> src/ab1_bak.rs:24:12 [INFO] [stdout] | [INFO] [stdout] 24 | #[cfg_attr(feature = "encode", derive(Encode, Decode))] [INFO] [stdout] | ^^^^^^^^^^-------- [INFO] [stdout] | | [INFO] [stdout] | help: there is a expected value with a similar name: `"bincode"` [INFO] [stdout] | [INFO] [stdout] = note: expected values for `feature` are: `bincode` [INFO] [stdout] = help: consider adding `encode` as a feature in `Cargo.toml` [INFO] [stdout] = note: see for more information about checking conditional configuration [INFO] [stdout] = note: `#[warn(unexpected_cfgs)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unexpected `cfg` condition value: `encode` [INFO] [stdout] --> src/ab1_bak.rs:15:7 [INFO] [stdout] | [INFO] [stdout] 15 | #[cfg(feature = "encode")] [INFO] [stdout] | ^^^^^^^^^^-------- [INFO] [stdout] | | [INFO] [stdout] | help: there is a expected value with a similar name: `"bincode"` [INFO] [stdout] | [INFO] [stdout] = note: expected values for `feature` are: `bincode` [INFO] [stdout] = help: consider adding `encode` as a feature in `Cargo.toml` [INFO] [stdout] = note: see for more information about checking conditional configuration [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::pileup_counter::PlpInfo` [INFO] [stdout] --> src/pileup_counter/mod.rs:255:9 [INFO] [stdout] | [INFO] [stdout] 255 | use crate::pileup_counter::PlpInfo; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unexpected `cfg` condition value: `encode` [INFO] [stdout] --> src/ab1_bak.rs:24:12 [INFO] [stdout] | [INFO] [stdout] 24 | #[cfg_attr(feature = "encode", derive(Encode, Decode))] [INFO] [stdout] | ^^^^^^^^^^-------- [INFO] [stdout] | | [INFO] [stdout] | help: there is a expected value with a similar name: `"bincode"` [INFO] [stdout] | [INFO] [stdout] = note: expected values for `feature` are: `bincode` [INFO] [stdout] = help: consider adding `encode` as a feature in `Cargo.toml` [INFO] [stdout] = note: see for more information about checking conditional configuration [INFO] [stdout] = note: `#[warn(unexpected_cfgs)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unexpected `cfg` condition value: `encode` [INFO] [stdout] --> src/ab1_bak.rs:15:7 [INFO] [stdout] | [INFO] [stdout] 15 | #[cfg(feature = "encode")] [INFO] [stdout] | ^^^^^^^^^^-------- [INFO] [stdout] | | [INFO] [stdout] | help: there is a expected value with a similar name: `"bincode"` [INFO] [stdout] | [INFO] [stdout] = note: expected values for `feature` are: `bincode` [INFO] [stdout] = help: consider adding `encode` as a feature in `Cargo.toml` [INFO] [stdout] = note: see for more information about checking conditional configuration [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `self` [INFO] [stdout] --> src/ab1_bak.rs:12:12 [INFO] [stdout] | [INFO] [stdout] 12 | path::{self, Path}, [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: `records` [INFO] [stdout] --> src/ab1_bak.rs:460:9 [INFO] [stdout] | [INFO] [stdout] 460 | let records = import_ab1(p).expect("import ab1 error"); [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_records` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `file_version`, `tag_name`, `tag_number`, `element_type_code`, and `data_size` are never read [INFO] [stdout] --> src/ab1_bak.rs:53:9 [INFO] [stdout] | [INFO] [stdout] 52 | struct Header { [INFO] [stdout] | ------ fields in this struct [INFO] [stdout] 53 | pub file_version: u16, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 54 | pub tag_name: Seq, // 4 bytes always. [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 55 | pub tag_number: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 56 | pub element_type_code: u16, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 59 | pub data_size: u32, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Header` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_abi_tag` is never used [INFO] [stdout] --> src/ab1_bak.rs:315:4 [INFO] [stdout] | [INFO] [stdout] 315 | fn parse_abi_tag(data: &[u8]) -> io::Result<(String, String)> { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `abi_trim` is never used [INFO] [stdout] --> src/ab1_bak.rs:325:4 [INFO] [stdout] | [INFO] [stdout] 325 | fn abi_trim(seq_record: &fastq::Record) -> fastq::Record { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `0` is never read [INFO] [stdout] --> src/ab1_bak.rs:382:9 [INFO] [stdout] | [INFO] [stdout] 382 | U32(Vec), [INFO] [stdout] | --- ^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | field in this variant [INFO] [stdout] | [INFO] [stdout] = note: `TagData` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] help: consider changing the field to be of unit type to suppress this warning while preserving the field numbering, or remove the field [INFO] [stdout] | [INFO] [stdout] 382 - U32(Vec), [INFO] [stdout] 382 + U32(()), [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `header` is never used [INFO] [stdout] --> src/ab1/ab1_file.rs:135:12 [INFO] [stdout] | [INFO] [stdout] 117 | impl AbiFileReader { [INFO] [stdout] | ------------------------------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 135 | pub fn header(&self) -> &Header { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `file_version`, `tag_name`, `tag_number`, `element_type_code`, and `data_size` are never read [INFO] [stdout] --> src/ab1_bak.rs:53:9 [INFO] [stdout] | [INFO] [stdout] 52 | struct Header { [INFO] [stdout] | ------ fields in this struct [INFO] [stdout] 53 | pub file_version: u16, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] 54 | pub tag_name: Seq, // 4 bytes always. [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 55 | pub tag_number: u32, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] 56 | pub element_type_code: u16, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 59 | pub data_size: u32, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Header` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_abi_tag` is never used [INFO] [stdout] --> src/ab1_bak.rs:315:4 [INFO] [stdout] | [INFO] [stdout] 315 | fn parse_abi_tag(data: &[u8]) -> io::Result<(String, String)> { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `abi_trim` is never used [INFO] [stdout] --> src/ab1_bak.rs:325:4 [INFO] [stdout] | [INFO] [stdout] 325 | fn abi_trim(seq_record: &fastq::Record) -> fastq::Record { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `0` is never read [INFO] [stdout] --> src/ab1_bak.rs:382:9 [INFO] [stdout] | [INFO] [stdout] 382 | U32(Vec), [INFO] [stdout] | --- ^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | field in this variant [INFO] [stdout] | [INFO] [stdout] = note: `TagData` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] help: consider changing the field to be of unit type to suppress this warning while preserving the field numbering, or remove the field [INFO] [stdout] | [INFO] [stdout] 382 - U32(Vec), [INFO] [stdout] 382 + U32(()), [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 37s [INFO] running `Command { std: "docker" "inspect" "9b504fac60add2a8ad54e2ee030fda6b53b3605bcaa73e84e201975fdc43dc03", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9b504fac60add2a8ad54e2ee030fda6b53b3605bcaa73e84e201975fdc43dc03", kill_on_drop: false }` [INFO] [stdout] 9b504fac60add2a8ad54e2ee030fda6b53b3605bcaa73e84e201975fdc43dc03