[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] 878a12c376d9c628d706e449a74f62655b6e66c7 [INFO] checking stela2502/quantify_bam against master#642c19bfc3a5c1de985bf5d0cc8207ac9d22708a for pr-148577 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-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-6-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/stela2502/quantify_bam on toolchain 642c19bfc3a5c1de985bf5d0cc8207ac9d22708a [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+642c19bfc3a5c1de985bf5d0cc8207ac9d22708a" "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" "+642c19bfc3a5c1de985bf5d0cc8207ac9d22708a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Updating git repository `https://github.com/stela2502/Rustody` [INFO] [stderr] Updating git repository `https://github.com/COMBINE-lab/kmers` [INFO] [stderr] Downloading crates ... 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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@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+642c19bfc3a5c1de985bf5d0cc8207ac9d22708a" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] ea4607d12686729d49c0589eac3a09a8998e759ec1fa8dba57c75f92c364fb41 [INFO] running `Command { std: "docker" "start" "-a" "ea4607d12686729d49c0589eac3a09a8998e759ec1fa8dba57c75f92c364fb41", kill_on_drop: false }` [INFO] [stderr] Compiling syn v2.0.98 [INFO] [stderr] Compiling libc v0.2.169 [INFO] [stderr] Checking miniz_oxide v0.8.3 [INFO] [stderr] Compiling glob v0.3.2 [INFO] [stderr] Checking lexical-util v0.8.5 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling libloading v0.8.6 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Checking 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[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: 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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) 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: 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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `fully_matched_exons` is never read [INFO] [stdout] --> src/gtf/gene.rs:139:21 [INFO] [stdout] | [INFO] [stdout] 139 | fully_matched_exons += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `fully_matched_exons` is never read [INFO] [stdout] --> src/gtf/gene.rs:177:21 [INFO] [stdout] | [INFO] [stdout] 177 | fully_matched_exons += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `fully_matched_exons` is never read [INFO] [stdout] --> src/gtf/gene.rs:139:21 [INFO] [stdout] | [INFO] [stdout] 139 | fully_matched_exons += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `fully_matched_exons` is never read [INFO] [stdout] --> src/gtf/gene.rs:177:21 [INFO] [stdout] | [INFO] [stdout] 177 | fully_matched_exons += 1; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(unused)]`) 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: 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: unused variable: `mate_gene_result` [INFO] [stdout] --> src/main_logics.rs:424:21 [INFO] [stdout] | [INFO] [stdout] 424 | let mate_gene_result = match match_type { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_result` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate_gene_result` [INFO] [stdout] --> src/main_logics.rs:424:21 [INFO] [stdout] | [INFO] [stdout] 424 | let mate_gene_result = match match_type { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_result` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate_gene_ids` [INFO] [stdout] --> src/main_logics.rs:439:21 [INFO] [stdout] | [INFO] [stdout] 439 | let mate_gene_ids = extract_gene_ids(&mate_gene_result, mate, mapping_info); [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_ids` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate_gene_ids` [INFO] [stdout] --> src/main_logics.rs:439:21 [INFO] [stdout] | [INFO] [stdout] 439 | let mate_gene_ids = extract_gene_ids(&mate_gene_result, mate, mapping_info); [INFO] [stdout] | ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_ids` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate_gene_id` [INFO] [stdout] --> src/main_logics.rs:441:21 [INFO] [stdout] | [INFO] [stdout] 441 | for mate_gene_id in &mate_gene_ids { [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_id` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate_gene_id` [INFO] [stdout] --> src/main_logics.rs:441:21 [INFO] [stdout] | [INFO] [stdout] 441 | for mate_gene_id in &mate_gene_ids { [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_id` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate_gene_id_u64` [INFO] [stdout] --> src/main_logics.rs:442:25 [INFO] [stdout] | [INFO] [stdout] 442 | let mate_gene_id_u64 = exp_idx.get_gene_id(mate_gene_id); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_id_u64` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate_guh` [INFO] [stdout] --> src/main_logics.rs:443:25 [INFO] [stdout] | [INFO] [stdout] 443 | let mate_guh = GeneUmiHash(mate_gene_id_u64, mate.umi); [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_guh` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `processor` [INFO] [stdout] --> src/main_logics.rs:446:37 [INFO] [stdout] | [INFO] [stdout] 446 | if let Some(processor) = mutations { [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_processor` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate_gene_id_u64` [INFO] [stdout] --> src/main_logics.rs:442:25 [INFO] [stdout] | [INFO] [stdout] 442 | let mate_gene_id_u64 = exp_idx.get_gene_id(mate_gene_id); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_id_u64` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `mate_guh` [INFO] [stdout] --> src/main_logics.rs:443:25 [INFO] [stdout] | [INFO] [stdout] 443 | let mate_guh = GeneUmiHash(mate_gene_id_u64, mate.umi); [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_guh` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `processor` [INFO] [stdout] --> src/main_logics.rs:446:37 [INFO] [stdout] | [INFO] [stdout] 446 | if let Some(processor) = mutations { [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_processor` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 30s [INFO] running `Command { std: "docker" "inspect" "ea4607d12686729d49c0589eac3a09a8998e759ec1fa8dba57c75f92c364fb41", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ea4607d12686729d49c0589eac3a09a8998e759ec1fa8dba57c75f92c364fb41", kill_on_drop: false }` [INFO] [stdout] ea4607d12686729d49c0589eac3a09a8998e759ec1fa8dba57c75f92c364fb41