[INFO] cloning repository https://github.com/stela2502/quantify_bam [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/stela2502/quantify_bam" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] efd1f6ab5ebc7197ac7629c5acb13fc06aebb110 [INFO] checking stela2502/quantify_bam against master#e9182f195b8505c87c4bd055b9f6e114ccda0981 for pr-144098 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam" "/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/quantify_bam [INFO] finished tweaking git repo https://github.com/stela2502/quantify_bam [INFO] tweaked toml for git repo https://github.com/stela2502/quantify_bam written to /workspace/builds/worker-7-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/stela2502/quantify_bam on toolchain e9182f195b8505c87c4bd055b9f6e114ccda0981 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+e9182f195b8505c87c4bd055b9f6e114ccda0981" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/stela2502/quantify_bam 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" "+e9182f195b8505c87c4bd055b9f6e114ccda0981" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Updating git repository `https://github.com/stela2502/Rustody` [INFO] [stderr] Updating git repository `https://github.com/COMBINE-lab/kmers` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded noodles-csi v0.13.0 [INFO] [stderr] Downloaded noodles-fasta v0.18.0 [INFO] [stderr] Downloaded derive-new v0.7.0 [INFO] [stderr] Downloaded noodles-bgzf v0.26.0 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded buffer-redux v1.0.2 [INFO] [stderr] Downloaded noodles-sam v0.23.0 [INFO] [stderr] Downloaded needletail v0.5.1 [INFO] [stderr] Downloaded noodles-core v0.10.0 [INFO] [stderr] Downloaded rust-htslib v0.49.0 [INFO] [stderr] Downloaded bzip2-sys v0.1.12+1.0.8 [INFO] [stderr] Downloaded curl-sys v0.4.79+curl-8.12.0 [INFO] [stderr] Downloaded hts-sys v2.2.0 [INFO] [stderr] Downloaded noodles-bam v0.26.0 [INFO] [stderr] Downloaded noodles-bgzf v0.19.0 [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:cf8efcab8866f2cf4285301c7418e2f4f2a9b088c91ba69c40d5b659f81557f7" "/opt/rustwide/cargo-home/bin/cargo" "+e9182f195b8505c87c4bd055b9f6e114ccda0981" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 97daf4b4b2fd9b602475ea2e7c506f24fcb723047dd187a19afd86d55ed4c91e [INFO] running `Command { std: "docker" "start" "-a" "97daf4b4b2fd9b602475ea2e7c506f24fcb723047dd187a19afd86d55ed4c91e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" 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"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:cf8efcab8866f2cf4285301c7418e2f4f2a9b088c91ba69c40d5b659f81557f7" "/opt/rustwide/cargo-home/bin/cargo" "+e9182f195b8505c87c4bd055b9f6e114ccda0981" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] f318338e7cd0ea315edc84156c8e65c33ffe312604646fe85fc442d09c3c09e0 [INFO] running `Command { std: "docker" "start" "-a" "f318338e7cd0ea315edc84156c8e65c33ffe312604646fe85fc442d09c3c09e0", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.93 [INFO] [stderr] Compiling unicode-ident v1.0.16 [INFO] [stderr] Compiling libc v0.2.169 [INFO] [stderr] Compiling shlex v1.3.0 [INFO] [stderr] Compiling pkg-config v0.3.31 [INFO] [stderr] Compiling autocfg v1.4.0 [INFO] [stderr] Checking cfg-if v1.0.0 [INFO] [stderr] Checking memchr v2.7.4 [INFO] [stderr] Compiling 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(https://github.com/stela2502/Rustody?branch=main2#edc49c8d) [INFO] [stderr] Checking rust-htslib v0.49.0 [INFO] [stderr] Checking quantify_bam v0.4.3 (/opt/rustwide/workdir) [INFO] [stdout] warning: unexpected `cfg` condition value: `write` [INFO] [stdout] --> src/value.rs:4:12 [INFO] [stdout] | [INFO] [stdout] 4 | #[cfg_attr(feature = "write", derive(Serialize, Deserialize))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: remove the condition [INFO] [stdout] | [INFO] [stdout] = note: no expected values for `feature` [INFO] [stdout] = help: consider adding `write` 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: unused import: `rustody::analysis::bam_flag::BamFlag` [INFO] [stdout] --> src/main_logics.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use rustody::analysis::bam_flag::BamFlag; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Cigar` and `Record` [INFO] [stdout] --> src/main_logics.rs:22:46 [INFO] [stdout] | [INFO] [stdout] 22 | use rust_htslib::bam::{Reader,Read, record::{Record, Cigar}}; [INFO] [stdout] | ^^^^^^ ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unexpected `cfg` condition value: `write` [INFO] [stdout] --> src/value.rs:4:12 [INFO] [stdout] | [INFO] [stdout] 4 | #[cfg_attr(feature = "write", derive(Serialize, Deserialize))] [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: remove the condition [INFO] [stdout] | [INFO] [stdout] = note: no expected values for `feature` [INFO] [stdout] = help: consider adding `write` 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: unused import: `rustody::analysis::bam_flag::BamFlag` [INFO] [stdout] --> src/main_logics.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use rustody::analysis::bam_flag::BamFlag; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Cigar` and `Record` [INFO] [stdout] --> src/main_logics.rs:22:46 [INFO] [stdout] | [INFO] [stdout] 22 | use rust_htslib::bam::{Reader,Read, record::{Record, Cigar}}; [INFO] [stdout] | ^^^^^^ ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable statement [INFO] [stdout] --> src/main_logics.rs:424:17 [INFO] [stdout] | [INFO] [stdout] 423 | todo!("Handle this case when I have more brainpower."); [INFO] [stdout] | ------------------------------------------------------ any code following this expression is unreachable [INFO] [stdout] 424 | / let mate_gene_result = match match_type { [INFO] [stdout] 425 | | MatchType::Overlap => gtf.match_cigar_to_gene_overlap( [INFO] [stdout] 426 | | &mate.chromosome, [INFO] [stdout] 427 | | &mate.cigar, [INFO] [stdout] ... | [INFO] [stdout] 436 | | ), [INFO] [stdout] 437 | | }; [INFO] [stdout] | |__________________^ unreachable statement [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unreachable_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unreachable statement [INFO] [stdout] --> src/main_logics.rs:424:17 [INFO] [stdout] | [INFO] [stdout] 423 | todo!("Handle this case when I have more brainpower."); [INFO] [stdout] | ------------------------------------------------------ any code following this expression is unreachable [INFO] [stdout] 424 | / let mate_gene_result = match match_type { [INFO] [stdout] 425 | | MatchType::Overlap => gtf.match_cigar_to_gene_overlap( [INFO] [stdout] 426 | | &mate.chromosome, [INFO] [stdout] 427 | | &mate.cigar, [INFO] [stdout] ... | [INFO] [stdout] 436 | | ), [INFO] [stdout] 437 | | }; [INFO] [stdout] | |__________________^ unreachable statement [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unreachable_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header_view` [INFO] [stdout] --> src/main_logics.rs:140:9 [INFO] [stdout] | [INFO] [stdout] 140 | let header_view = Header::from_template(reader.header() ); [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_header_view` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header_view` [INFO] [stdout] --> src/main_logics.rs:140:9 [INFO] [stdout] | [INFO] [stdout] 140 | let header_view = Header::from_template(reader.header() ); [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_header_view` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main_logics.rs:139:9 [INFO] [stdout] | [INFO] [stdout] 139 | let mut reader = Reader::from_path( bam_file ).unwrap(); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate` [INFO] [stdout] --> src/main_logics.rs:422:25 [INFO] [stdout] | [INFO] [stdout] 422 | if let Some(mate) = mate_read { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_mate` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main_logics.rs:139:9 [INFO] [stdout] | [INFO] [stdout] 139 | let mut reader = Reader::from_path( bam_file ).unwrap(); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate` [INFO] [stdout] --> src/main_logics.rs:422:25 [INFO] [stdout] | [INFO] [stdout] 422 | if let Some(mate) = mate_read { [INFO] [stdout] | ^^^^ help: if this is intentional, prefix it with an underscore: `_mate` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 04s [INFO] running `Command { std: "docker" "inspect" "f318338e7cd0ea315edc84156c8e65c33ffe312604646fe85fc442d09c3c09e0", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f318338e7cd0ea315edc84156c8e65c33ffe312604646fe85fc442d09c3c09e0", kill_on_drop: false }` [INFO] [stdout] f318338e7cd0ea315edc84156c8e65c33ffe312604646fe85fc442d09c3c09e0