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[INFO] [stderr] Downloaded clap v4.4.1 [INFO] [stderr] Downloaded clap_builder v4.4.1 [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:c80049f3b88b82089a44e0f06d0d6029d44b96b7257e55a1cd63dbc9f4c33334" "/opt/rustwide/cargo-home/bin/cargo" "+cd805f09ffbfa3896c8f50a619de9b67e1d9f3c3" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 0645617d469ffcdefcf17f6e5abfcfa6de72cc4dbcd9641a515605c6086aac2f [INFO] running `Command { std: "docker" "start" "-a" "0645617d469ffcdefcf17f6e5abfcfa6de72cc4dbcd9641a515605c6086aac2f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "0645617d469ffcdefcf17f6e5abfcfa6de72cc4dbcd9641a515605c6086aac2f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "0645617d469ffcdefcf17f6e5abfcfa6de72cc4dbcd9641a515605c6086aac2f", kill_on_drop: false }` [INFO] [stdout] 0645617d469ffcdefcf17f6e5abfcfa6de72cc4dbcd9641a515605c6086aac2f [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:c80049f3b88b82089a44e0f06d0d6029d44b96b7257e55a1cd63dbc9f4c33334" "/opt/rustwide/cargo-home/bin/cargo" "+cd805f09ffbfa3896c8f50a619de9b67e1d9f3c3" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] e4a3b70cd697e689035c40a553139bbbe01bd32a1fbe3162c3f10bd88d607d50 [INFO] running `Command { std: "docker" "start" "-a" "e4a3b70cd697e689035c40a553139bbbe01bd32a1fbe3162c3f10bd88d607d50", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.66 [INFO] [stderr] Compiling unicode-ident v1.0.11 [INFO] [stderr] Checking utf8parse v0.2.1 [INFO] [stderr] Checking anstyle-query v1.0.0 [INFO] [stderr] Checking colorchoice v1.0.0 [INFO] [stderr] Checking memchr v2.6.1 [INFO] [stderr] Checking anstyle v1.0.2 [INFO] [stderr] Compiling heck v0.4.1 [INFO] [stderr] Checking clap_lex v0.5.1 [INFO] [stderr] Checking strsim v0.10.0 [INFO] [stderr] Checking regex-syntax v0.7.5 [INFO] [stderr] Compiling anyhow v1.0.75 [INFO] [stderr] Checking once_cell v1.18.0 [INFO] [stderr] Checking anstyle-parse v0.2.1 [INFO] [stderr] Checking aho-corasick v1.0.5 [INFO] [stderr] Checking anstream v0.5.0 [INFO] [stderr] Checking clap_builder v4.4.1 [INFO] [stderr] Compiling quote v1.0.33 [INFO] [stderr] Compiling syn v2.0.29 [INFO] [stderr] Checking regex-automata v0.3.7 [INFO] [stderr] Compiling clap_derive v4.4.0 [INFO] [stderr] Checking regex v1.9.4 [INFO] [stderr] Checking clap v4.4.1 [INFO] [stderr] Checking ervcaller-rs v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `anyhow` [INFO] [stdout] --> src/main.rs:1:14 [INFO] [stdout] | [INFO] [stdout] 1 | use anyhow::{anyhow, Error, Result}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::f32::consts::E` [INFO] [stdout] --> src/main.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::f32::consts::E; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `PathBuf` [INFO] [stdout] --> src/main.rs:7:23 [INFO] [stdout] | [INFO] [stdout] 7 | use std::path::{Path, PathBuf}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ExitStatus` [INFO] [stdout] --> src/main.rs:8:29 [INFO] [stdout] | [INFO] [stdout] 8 | use std::process::{Command, ExitStatus}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused doc comment [INFO] [stdout] --> src/main.rs:183:5 [INFO] [stdout] | [INFO] [stdout] 183 | /// create output director passed from cli args if not exists [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 184 | / if let Err(err) = create_directory_if_not_exists(&args.output_directory) { [INFO] [stdout] 185 | | eprintln!("Failed to create directory: {}", err); [INFO] [stdout] 186 | | } [INFO] [stdout] | |_____- rustdoc does not generate documentation for expressions [INFO] [stdout] | [INFO] [stdout] = help: use `//` for a plain comment [INFO] [stdout] = note: `#[warn(unused_doc_comments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `anyhow` [INFO] [stdout] --> src/main.rs:1:14 [INFO] [stdout] | [INFO] [stdout] 1 | use anyhow::{anyhow, Error, Result}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::f32::consts::E` [INFO] [stdout] --> src/main.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::f32::consts::E; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `PathBuf` [INFO] [stdout] --> src/main.rs:7:23 [INFO] [stdout] | [INFO] [stdout] 7 | use std::path::{Path, PathBuf}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ExitStatus` [INFO] [stdout] --> src/main.rs:8:29 [INFO] [stdout] | [INFO] [stdout] 8 | use std::process::{Command, ExitStatus}; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused doc comment [INFO] [stdout] --> src/main.rs:183:5 [INFO] [stdout] | [INFO] [stdout] 183 | /// create output director passed from cli args if not exists [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 184 | / if let Err(err) = create_directory_if_not_exists(&args.output_directory) { [INFO] [stdout] 185 | | eprintln!("Failed to create directory: {}", err); [INFO] [stdout] 186 | | } [INFO] [stdout] | |_____- rustdoc does not generate documentation for expressions [INFO] [stdout] | [INFO] [stdout] = help: use `//` for a plain comment [INFO] [stdout] = note: `#[warn(unused_doc_comments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `std_insert_size` is assigned to, but never used [INFO] [stdout] --> src/main.rs:99:13 [INFO] [stdout] | [INFO] [stdout] 99 | let mut std_insert_size: f32 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_std_insert_size` instead [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bowtie2_d` [INFO] [stdout] --> src/main.rs:107:9 [INFO] [stdout] | [INFO] [stdout] 107 | let bowtie2_d = ""; [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bowtie2_d` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `tophat_d` [INFO] [stdout] --> src/main.rs:108:9 [INFO] [stdout] | [INFO] [stdout] 108 | let tophat_d = ""; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tophat_d` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `se_mei_d` [INFO] [stdout] --> src/main.rs:111:9 [INFO] [stdout] | [INFO] [stdout] 111 | let se_mei_d = ""; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_se_mei_d` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `std_insert_size` is never read [INFO] [stdout] --> src/main.rs:117:9 [INFO] [stdout] | [INFO] [stdout] 117 | std_insert_size = args.l_std_insert_size.unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `tsd_min_len` [INFO] [stdout] --> src/main.rs:168:13 [INFO] [stdout] | [INFO] [stdout] 168 | let mut tsd_min_len = 100; [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tsd_min_len` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `human_genome` [INFO] [stdout] --> src/main.rs:170:13 [INFO] [stdout] | [INFO] [stdout] 170 | let mut human_genome = &args.human_reference_genome; [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_human_genome` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `human_genome_tophat` [INFO] [stdout] --> src/main.rs:171:13 [INFO] [stdout] | [INFO] [stdout] 171 | let mut human_genome_tophat = &args.human_reference_genome; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_human_genome_tophat` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `genome` [INFO] [stdout] --> src/main.rs:173:13 [INFO] [stdout] | [INFO] [stdout] 173 | let mut genome: HashMap = HashMap::new(); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_genome` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `order` is assigned to, but never used [INFO] [stdout] --> src/main.rs:174:13 [INFO] [stdout] | [INFO] [stdout] 174 | let mut order = 0; [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_order` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_insertsize` [INFO] [stdout] --> src/main.rs:175:9 [INFO] [stdout] | [INFO] [stdout] 175 | let min_insertsize = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_insertsize` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `thread_1` [INFO] [stdout] --> src/main.rs:176:9 [INFO] [stdout] | [INFO] [stdout] 176 | let thread_1 = args.threads.unwrap() - 1; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_thread_1` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `double_length_insertsize` [INFO] [stdout] --> src/main.rs:177:9 [INFO] [stdout] | [INFO] [stdout] 177 | let double_length_insertsize = 0.0f64; // Define the correct type [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_double_length_insertsize` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `cmd` [INFO] [stdout] --> src/main.rs:178:9 [INFO] [stdout] | [INFO] [stdout] 178 | let cmd = String::new(); // You can use String for dynamic strings [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_cmd` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bp1_tmp3` [INFO] [stdout] --> src/main.rs:179:13 [INFO] [stdout] | [INFO] [stdout] 179 | let mut bp1_tmp3: Vec = Vec::new(); // Define the correct type [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bp1_tmp3` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header3` [INFO] [stdout] --> src/main.rs:180:9 [INFO] [stdout] | [INFO] [stdout] 180 | let header3 = "Sample_ID Is_Split_mode ... Genotype\n".to_string(); [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_header3` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `order` [INFO] [stdout] --> src/main.rs:281:13 [INFO] [stdout] | [INFO] [stdout] 281 | let order = 1; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_order` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `order` [INFO] [stdout] --> src/main.rs:285:17 [INFO] [stdout] | [INFO] [stdout] 285 | let order = 2; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_order` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `order` is never read [INFO] [stdout] --> src/main.rs:360:9 [INFO] [stdout] | [INFO] [stdout] 360 | order = 0; [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.rs:168:9 [INFO] [stdout] | [INFO] [stdout] 168 | let mut tsd_min_len = 100; [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: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:169:9 [INFO] [stdout] | [INFO] [stdout] 169 | let mut alignment_score = 30; [INFO] [stdout] | ----^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:170:9 [INFO] [stdout] | [INFO] [stdout] 170 | let mut human_genome = &args.human_reference_genome; [INFO] [stdout] | ----^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:171:9 [INFO] [stdout] | [INFO] [stdout] 171 | let mut human_genome_tophat = &args.human_reference_genome; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:173:9 [INFO] [stdout] | [INFO] [stdout] 173 | let mut genome: HashMap = HashMap::new(); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:179:9 [INFO] [stdout] | [INFO] [stdout] 179 | let mut bp1_tmp3: Vec = Vec::new(); // Define the correct type [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `std_insert_size` is assigned to, but never used [INFO] [stdout] --> src/main.rs:99:13 [INFO] [stdout] | [INFO] [stdout] 99 | let mut std_insert_size: f32 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_std_insert_size` instead [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bowtie2_d` [INFO] [stdout] --> src/main.rs:107:9 [INFO] [stdout] | [INFO] [stdout] 107 | let bowtie2_d = ""; [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bowtie2_d` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `tophat_d` [INFO] [stdout] --> src/main.rs:108:9 [INFO] [stdout] | [INFO] [stdout] 108 | let tophat_d = ""; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tophat_d` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `se_mei_d` [INFO] [stdout] --> src/main.rs:111:9 [INFO] [stdout] | [INFO] [stdout] 111 | let se_mei_d = ""; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_se_mei_d` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `std_insert_size` is never read [INFO] [stdout] --> src/main.rs:117:9 [INFO] [stdout] | [INFO] [stdout] 117 | std_insert_size = args.l_std_insert_size.unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `tsd_min_len` [INFO] [stdout] --> src/main.rs:168:13 [INFO] [stdout] | [INFO] [stdout] 168 | let mut tsd_min_len = 100; [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_tsd_min_len` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `human_genome` [INFO] [stdout] --> src/main.rs:170:13 [INFO] [stdout] | [INFO] [stdout] 170 | let mut human_genome = &args.human_reference_genome; [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_human_genome` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `human_genome_tophat` [INFO] [stdout] --> src/main.rs:171:13 [INFO] [stdout] | [INFO] [stdout] 171 | let mut human_genome_tophat = &args.human_reference_genome; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_human_genome_tophat` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `genome` [INFO] [stdout] --> src/main.rs:173:13 [INFO] [stdout] | [INFO] [stdout] 173 | let mut genome: HashMap = HashMap::new(); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_genome` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `order` is assigned to, but never used [INFO] [stdout] --> src/main.rs:174:13 [INFO] [stdout] | [INFO] [stdout] 174 | let mut order = 0; [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_order` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_insertsize` [INFO] [stdout] --> src/main.rs:175:9 [INFO] [stdout] | [INFO] [stdout] 175 | let min_insertsize = 0; [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_insertsize` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `thread_1` [INFO] [stdout] --> src/main.rs:176:9 [INFO] [stdout] | [INFO] [stdout] 176 | let thread_1 = args.threads.unwrap() - 1; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_thread_1` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `double_length_insertsize` [INFO] [stdout] --> src/main.rs:177:9 [INFO] [stdout] | [INFO] [stdout] 177 | let double_length_insertsize = 0.0f64; // Define the correct type [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_double_length_insertsize` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `cmd` [INFO] [stdout] --> src/main.rs:178:9 [INFO] [stdout] | [INFO] [stdout] 178 | let cmd = String::new(); // You can use String for dynamic strings [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_cmd` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bp1_tmp3` [INFO] [stdout] --> src/main.rs:179:13 [INFO] [stdout] | [INFO] [stdout] 179 | let mut bp1_tmp3: Vec = Vec::new(); // Define the correct type [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bp1_tmp3` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `header3` [INFO] [stdout] --> src/main.rs:180:9 [INFO] [stdout] | [INFO] [stdout] 180 | let header3 = "Sample_ID Is_Split_mode ... Genotype\n".to_string(); [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_header3` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `order` [INFO] [stdout] --> src/main.rs:281:13 [INFO] [stdout] | [INFO] [stdout] 281 | let order = 1; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_order` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `order` [INFO] [stdout] --> src/main.rs:285:17 [INFO] [stdout] | [INFO] [stdout] 285 | let order = 2; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_order` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `order` is never read [INFO] [stdout] --> src/main.rs:360:9 [INFO] [stdout] | [INFO] [stdout] 360 | order = 0; [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `format` [INFO] [stdout] --> src/main.rs:610:16 [INFO] [stdout] | [INFO] [stdout] 610 | fn align_to_hg(format: &str, arg: &str) { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_format` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `arg` [INFO] [stdout] --> src/main.rs:610:30 [INFO] [stdout] | [INFO] [stdout] 610 | fn align_to_hg(format: &str, arg: &str) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_arg` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `input_sample_id` [INFO] [stdout] --> src/main.rs:614:23 [INFO] [stdout] | [INFO] [stdout] 614 | fn convert_bamtofastq(input_sample_id: &str) { [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_sample_id` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_as_xs` is never used [INFO] [stdout] --> src/main.rs:566:4 [INFO] [stdout] | [INFO] [stdout] 566 | fn parse_as_xs(line: &str) -> (&str, &str) { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `aS` should have a snake case name [INFO] [stdout] --> src/main.rs:528:17 [INFO] [stdout] | [INFO] [stdout] 528 | let mut aS = "NA"; [INFO] [stdout] | ^^ help: convert the identifier to snake case: `a_s` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `aS` should have a snake case name [INFO] [stdout] --> src/main.rs:567:13 [INFO] [stdout] | [INFO] [stdout] 567 | let mut aS = "NA"; [INFO] [stdout] | ^^ help: convert the identifier to snake case: `a_s` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:168:9 [INFO] [stdout] | [INFO] [stdout] 168 | let mut tsd_min_len = 100; [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: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:169:9 [INFO] [stdout] | [INFO] [stdout] 169 | let mut alignment_score = 30; [INFO] [stdout] | ----^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:170:9 [INFO] [stdout] | [INFO] [stdout] 170 | let mut human_genome = &args.human_reference_genome; [INFO] [stdout] | ----^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:171:9 [INFO] [stdout] | [INFO] [stdout] 171 | let mut human_genome_tophat = &args.human_reference_genome; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:173:9 [INFO] [stdout] | [INFO] [stdout] 173 | let mut genome: HashMap = HashMap::new(); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:179:9 [INFO] [stdout] | [INFO] [stdout] 179 | let mut bp1_tmp3: Vec = Vec::new(); // Define the correct type [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `format` [INFO] [stdout] --> src/main.rs:610:16 [INFO] [stdout] | [INFO] [stdout] 610 | fn align_to_hg(format: &str, arg: &str) { [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_format` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `arg` [INFO] [stdout] --> src/main.rs:610:30 [INFO] [stdout] | [INFO] [stdout] 610 | fn align_to_hg(format: &str, arg: &str) { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_arg` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `input_sample_id` [INFO] [stdout] --> src/main.rs:614:23 [INFO] [stdout] | [INFO] [stdout] 614 | fn convert_bamtofastq(input_sample_id: &str) { [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_sample_id` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parse_as_xs` is never used [INFO] [stdout] --> src/main.rs:566:4 [INFO] [stdout] | [INFO] [stdout] 566 | fn parse_as_xs(line: &str) -> (&str, &str) { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `aS` should have a snake case name [INFO] [stdout] --> src/main.rs:528:17 [INFO] [stdout] | [INFO] [stdout] 528 | let mut aS = "NA"; [INFO] [stdout] | ^^ help: convert the identifier to snake case: `a_s` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `aS` should have a snake case name [INFO] [stdout] --> src/main.rs:567:13 [INFO] [stdout] | [INFO] [stdout] 567 | let mut aS = "NA"; [INFO] [stdout] | ^^ help: convert the identifier to snake case: `a_s` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 9.88s [INFO] running `Command { std: "docker" "inspect" "e4a3b70cd697e689035c40a553139bbbe01bd32a1fbe3162c3f10bd88d607d50", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e4a3b70cd697e689035c40a553139bbbe01bd32a1fbe3162c3f10bd88d607d50", kill_on_drop: false }` [INFO] [stdout] e4a3b70cd697e689035c40a553139bbbe01bd32a1fbe3162c3f10bd88d607d50