[INFO] fetching crate bioutils 0.2.0... [INFO] checking bioutils-0.2.0 against try#3bb2879ea9e58d65b875f9a98df44f4a43ce2597 for pr-85387 [INFO] extracting crate bioutils 0.2.0 into /workspace/builds/worker-0/source [INFO] validating manifest of crates.io crate bioutils 0.2.0 on toolchain 3bb2879ea9e58d65b875f9a98df44f4a43ce2597 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+3bb2879ea9e58d65b875f9a98df44f4a43ce2597" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate bioutils 0.2.0 [INFO] finished tweaking crates.io crate bioutils 0.2.0 [INFO] tweaked toml for crates.io crate bioutils 0.2.0 written to /workspace/builds/worker-0/source/Cargo.toml [INFO] crate crates.io crate bioutils 0.2.0 already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+3bb2879ea9e58d65b875f9a98df44f4a43ce2597" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded cfb v0.4.0 [INFO] [stderr] Downloaded infer v0.4.0 [INFO] [stderr] Downloaded suffix_array v0.5.0 [INFO] [stderr] Downloaded sacabase v2.0.0 [INFO] [stderr] Downloaded packed_simd_2 v0.3.4 [INFO] [stderr] Downloaded seq_io v0.3.1 [INFO] [stderr] Downloaded cdivsufsort v2.0.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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@sha256:20528e8c29e4536546f0102ce88568b16ea7538393a33fcca951030f7af10457" "/opt/rustwide/cargo-home/bin/cargo" "+3bb2879ea9e58d65b875f9a98df44f4a43ce2597" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] e3b65a4eca77c2ea44ce6413341509691fdfca8185c5c86c255aa38a12896923 [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "e3b65a4eca77c2ea44ce6413341509691fdfca8185c5c86c255aa38a12896923", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "e3b65a4eca77c2ea44ce6413341509691fdfca8185c5c86c255aa38a12896923", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e3b65a4eca77c2ea44ce6413341509691fdfca8185c5c86c255aa38a12896923", kill_on_drop: false }` [INFO] [stdout] e3b65a4eca77c2ea44ce6413341509691fdfca8185c5c86c255aa38a12896923 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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" "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@sha256:20528e8c29e4536546f0102ce88568b16ea7538393a33fcca951030f7af10457" "/opt/rustwide/cargo-home/bin/cargo" "+3bb2879ea9e58d65b875f9a98df44f4a43ce2597" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] 32cca7dae4f10c168544abd10249f7a493332f7ca32c02197259950355a2e6c7 [INFO] running `Command { std: "docker" "start" "-a" "32cca7dae4f10c168544abd10249f7a493332f7ca32c02197259950355a2e6c7", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling libc v0.2.86 [INFO] [stderr] Checking cfg-if v1.0.0 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Compiling log v0.4.14 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Compiling syn v1.0.64 [INFO] [stderr] Compiling winapi-build v0.1.1 [INFO] [stderr] Checking fnv v1.0.7 [INFO] [stderr] Checking foreign-types-shared v0.1.1 [INFO] [stderr] Compiling openssl v0.10.33 [INFO] [stderr] Checking byteorder v1.4.3 [INFO] [stderr] Checking winapi v0.2.8 [INFO] [stderr] Compiling httparse v1.3.5 [INFO] [stderr] Checking futures-sink v0.3.13 [INFO] [stderr] Compiling serde v1.0.125 [INFO] [stderr] Checking futures-task v0.3.13 [INFO] [stderr] Compiling crc32fast v1.2.1 [INFO] [stderr] Checking adler v1.0.2 [INFO] [stderr] Checking either v1.6.1 [INFO] [stderr] Checking adler32 v1.2.0 [INFO] [stderr] Compiling curl v0.4.34 [INFO] [stderr] Checking regex-syntax v0.3.9 [INFO] [stderr] Checking uuid v0.8.2 [INFO] [stderr] Checking utf8-ranges v0.1.3 [INFO] [stderr] Checking safemem v0.3.3 [INFO] [stderr] Checking lazy_static v0.1.16 [INFO] [stderr] Checking bytecount v0.6.2 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling curl-sys v0.4.40+curl-7.75.0 [INFO] [stderr] Compiling cdivsufsort v2.0.0 [INFO] [stderr] Checking futures-channel v0.3.13 [INFO] [stderr] Checking tinyvec v1.1.1 [INFO] [stderr] Checking http v0.2.3 [INFO] [stderr] Checking tracing-core v0.1.17 [INFO] [stderr] Checking form_urlencoded v1.0.1 [INFO] [stderr] Checking foreign-types v0.3.2 [INFO] [stderr] Checking miniz_oxide v0.3.7 [INFO] [stderr] Checking futures-util v0.3.13 [INFO] [stderr] Checking deflate v0.8.6 [INFO] [stderr] Compiling kernel32-sys v0.2.2 [INFO] [stderr] Checking cfb v0.4.0 [INFO] [stderr] Checking encoding_rs v0.8.28 [INFO] [stderr] Checking buf_redux v0.8.4 [INFO] [stderr] Checking regex v1.4.6 [INFO] [stderr] Compiling openssl-sys v0.9.61 [INFO] [stderr] Compiling crossbeam-utils v0.8.3 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling memoffset v0.6.3 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling tokio v1.4.0 [INFO] [stderr] Compiling num-iter v0.1.42 [INFO] [stderr] Compiling indexmap v1.6.2 [INFO] [stderr] Compiling miniz_oxide v0.4.4 [INFO] [stderr] Compiling rayon v1.5.0 [INFO] [stderr] Compiling num-rational v0.3.2 [INFO] [stderr] Checking tracing v0.1.25 [INFO] [stderr] Checking want v0.3.0 [INFO] [stderr] Checking mio v0.7.11 [INFO] [stderr] Checking num_cpus v1.13.0 [INFO] [stderr] Checking socket2 v0.3.19 [INFO] [stderr] Checking memchr v0.1.11 [INFO] [stderr] Checking getrandom v0.2.2 [INFO] [stderr] Checking time v0.1.43 [INFO] [stderr] Checking infer v0.4.0 [INFO] [stderr] Checking unicode-normalization v0.1.17 [INFO] [stderr] Checking png v0.16.8 [INFO] [stderr] Checking rand_core v0.6.2 [INFO] [stderr] Checking aho-corasick v0.5.3 [INFO] [stderr] Checking thread-id v2.0.0 [INFO] [stderr] Checking rand_chacha v0.3.0 [INFO] [stderr] Checking thread_local v0.2.7 [INFO] [stderr] Compiling native-tls v0.2.7 [INFO] [stderr] Checking http-body v0.4.1 [INFO] [stderr] Checking regex v0.1.80 [INFO] [stderr] Checking crossbeam-epoch v0.9.3 [INFO] [stderr] Checking crossbeam-channel v0.5.0 [INFO] [stderr] Checking crossbeam-queue v0.3.1 [INFO] [stderr] Checking rand v0.8.3 [INFO] [stderr] Checking idna v0.2.2 [INFO] [stderr] Checking crossbeam-deque v0.8.0 [INFO] [stderr] Checking flate2 v1.0.20 [INFO] [stderr] Checking sacabase v2.0.0 [INFO] [stderr] Checking rayon-core v1.9.0 [INFO] [stderr] Checking crossbeam v0.8.0 [INFO] [stderr] Checking suffix_array v0.5.0 [INFO] [stderr] Checking url v2.2.1 [INFO] [stderr] Checking num v0.1.42 [INFO] [stderr] Checking chrono v0.2.25 [INFO] [stderr] Checking serde_urlencoded v0.7.0 [INFO] [stderr] Checking ftp v3.0.1 [INFO] [stderr] Checking tokio-util v0.6.5 [INFO] [stderr] Checking tokio-native-tls v0.3.0 [INFO] [stderr] Checking jpeg-decoder v0.1.22 [INFO] [stderr] Checking h2 v0.3.2 [INFO] [stderr] Checking tiff v0.6.1 [INFO] [stderr] Compiling pin-project-internal v1.0.6 [INFO] [stderr] Compiling serde_derive v1.0.125 [INFO] [stderr] Checking image v0.23.14 [INFO] [stderr] Checking pin-project v1.0.6 [INFO] [stderr] Checking hyper v0.14.4 [INFO] [stderr] Checking hyper-tls v0.5.0 [INFO] [stderr] Checking reqwest v0.11.2 [INFO] [stderr] Checking seq_io v0.3.1 [INFO] [stderr] Checking bioutils v0.2.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused imports: `Cursor`, `Read`, `self` [INFO] [stdout] --> src/files/fastq/hash.rs:4:15 [INFO] [stdout] | [INFO] [stdout] 4 | use std::io::{self, Cursor, Read}; [INFO] [stdout] | ^^^^ ^^^^^^ ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::iter::FromIterator` [INFO] [stdout] --> src/files/fastq/hash.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use std::iter::FromIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Reader` [INFO] [stdout] --> src/files/fastq/hash.rs:6:21 [INFO] [stdout] | [INFO] [stdout] 6 | use seq_io::fastq::{Reader,Record}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/files/fastq/hash.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::BufWriter` [INFO] [stdout] --> src/files/fastq/hash.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use std::io::BufWriter; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::Error` [INFO] [stdout] --> src/files/infer.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::io::Error; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/files/infer.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::BufReader` [INFO] [stdout] --> src/files/infer.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::io::BufReader; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `infer::Type` [INFO] [stdout] --> src/files/infer.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use infer::Type; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `infer::get_from_path` [INFO] [stdout] --> src/files/infer.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use infer::get_from_path; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::borrow::Borrow` [INFO] [stdout] --> src/utils/check/value.rs:33:5 [INFO] [stdout] | [INFO] [stdout] 33 | use std::borrow::Borrow; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/utils/check/value.rs:36:5 [INFO] [stdout] | [INFO] [stdout] 36 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::charsets::PERCENTAGE_RANGE` [INFO] [stdout] --> src/utils/check/value.rs:37:5 [INFO] [stdout] | [INFO] [stdout] 37 | use crate::charsets::PERCENTAGE_RANGE; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::utils::get::value` [INFO] [stdout] --> src/utils/check/value.rs:40:5 [INFO] [stdout] | [INFO] [stdout] 40 | use crate::utils::get::value; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::iter::FromIterator` [INFO] [stdout] --> src/utils/get/item.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use std::iter::FromIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bytecount::count` [INFO] [stdout] --> src/utils/get/value.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use bytecount::count; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::charsets::quality::*` [INFO] [stdout] --> src/utils/get/value.rs:21:5 [INFO] [stdout] | [INFO] [stdout] 21 | use crate::charsets::quality::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::rngs::ThreadRng` [INFO] [stdout] --> src/utils/get/value.rs:22:5 [INFO] [stdout] | [INFO] [stdout] 22 | use rand::rngs::ThreadRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::seq::SliceRandom` [INFO] [stdout] --> src/utils/get/value.rs:23:5 [INFO] [stdout] | [INFO] [stdout] 23 | use rand::seq::SliceRandom; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::convert::TryInto` [INFO] [stdout] --> src/utils/get/value.rs:24:5 [INFO] [stdout] | [INFO] [stdout] 24 | use std::convert::TryInto; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ImageBuffer` [INFO] [stdout] --> src/utils/image/color.rs:14:13 [INFO] [stdout] | [INFO] [stdout] 14 | use image::{ImageBuffer, Rgb}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `Cursor`, `Read`, `self` [INFO] [stdout] --> src/files/fastq/hash.rs:4:15 [INFO] [stdout] | [INFO] [stdout] 4 | use std::io::{self, Cursor, Read}; [INFO] [stdout] | ^^^^ ^^^^^^ ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::iter::FromIterator` [INFO] [stdout] --> src/files/fastq/hash.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use std::iter::FromIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Reader` [INFO] [stdout] --> src/files/fastq/hash.rs:6:21 [INFO] [stdout] | [INFO] [stdout] 6 | use seq_io::fastq::{Reader,Record}; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/files/fastq/hash.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::BufWriter` [INFO] [stdout] --> src/files/fastq/hash.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use std::io::BufWriter; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::Error` [INFO] [stdout] --> src/files/infer.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::io::Error; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> src/files/infer.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::io::BufReader` [INFO] [stdout] --> src/files/infer.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::io::BufReader; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `infer::Type` [INFO] [stdout] --> src/files/infer.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use infer::Type; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `infer::get_from_path` [INFO] [stdout] --> src/files/infer.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use infer::get_from_path; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::borrow::Borrow` [INFO] [stdout] --> src/utils/check/value.rs:33:5 [INFO] [stdout] | [INFO] [stdout] 33 | use std::borrow::Borrow; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::collections::HashMap` [INFO] [stdout] --> src/utils/check/value.rs:36:5 [INFO] [stdout] | [INFO] [stdout] 36 | use std::collections::HashMap; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::charsets::PERCENTAGE_RANGE` [INFO] [stdout] --> src/utils/check/value.rs:37:5 [INFO] [stdout] | [INFO] [stdout] 37 | use crate::charsets::PERCENTAGE_RANGE; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::utils::get::value` [INFO] [stdout] --> src/utils/check/value.rs:40:5 [INFO] [stdout] | [INFO] [stdout] 40 | use crate::utils::get::value; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::iter::FromIterator` [INFO] [stdout] --> src/utils/get/item.rs:10:5 [INFO] [stdout] | [INFO] [stdout] 10 | use std::iter::FromIterator; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bytecount::count` [INFO] [stdout] --> src/utils/get/value.rs:17:5 [INFO] [stdout] | [INFO] [stdout] 17 | use bytecount::count; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::charsets::quality::*` [INFO] [stdout] --> src/utils/get/value.rs:21:5 [INFO] [stdout] | [INFO] [stdout] 21 | use crate::charsets::quality::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::rngs::ThreadRng` [INFO] [stdout] --> src/utils/get/value.rs:22:5 [INFO] [stdout] | [INFO] [stdout] 22 | use rand::rngs::ThreadRng; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rand::seq::SliceRandom` [INFO] [stdout] --> src/utils/get/value.rs:23:5 [INFO] [stdout] | [INFO] [stdout] 23 | use rand::seq::SliceRandom; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::convert::TryInto` [INFO] [stdout] --> src/utils/get/value.rs:24:5 [INFO] [stdout] | [INFO] [stdout] 24 | use std::convert::TryInto; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ImageBuffer` [INFO] [stdout] --> src/utils/image/color.rs:14:13 [INFO] [stdout] | [INFO] [stdout] 14 | use image::{ImageBuffer, Rgb}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `record` [INFO] [stdout] --> src/files/fastq/hash.rs:18:17 [INFO] [stdout] | [INFO] [stdout] 18 | Err(record) => continue [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_record` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `record` [INFO] [stdout] --> src/files/fastq/hash.rs:57:17 [INFO] [stdout] | [INFO] [stdout] 57 | Err(record) => continue [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_record` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `num` [INFO] [stdout] --> src/utils/hashmap/value.rs:30:79 [INFO] [stdout] | [INFO] [stdout] 30 | pub fn value_cosine(hm1: &HashMap, u64>, hm2: &HashMap, u64>, num: Vec) -> f64 { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_num` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `num` [INFO] [stdout] --> src/utils/hashmap/value.rs:39:74 [INFO] [stdout] | [INFO] [stdout] 39 | pub fn jaccard(hm1: &HashMap, u64>, hm2: &HashMap, u64>, num: Vec) -> f64 { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_num` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `record` [INFO] [stdout] --> src/files/fastq/hash.rs:18:17 [INFO] [stdout] | [INFO] [stdout] 18 | Err(record) => continue [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_record` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `record` [INFO] [stdout] --> src/files/fastq/hash.rs:57:17 [INFO] [stdout] | [INFO] [stdout] 57 | Err(record) => continue [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_record` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `num` [INFO] [stdout] --> src/utils/hashmap/value.rs:30:79 [INFO] [stdout] | [INFO] [stdout] 30 | pub fn value_cosine(hm1: &HashMap, u64>, hm2: &HashMap, u64>, num: Vec) -> f64 { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_num` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `num` [INFO] [stdout] --> src/utils/hashmap/value.rs:39:74 [INFO] [stdout] | [INFO] [stdout] 39 | pub fn jaccard(hm1: &HashMap, u64>, hm2: &HashMap, u64>, num: Vec) -> f64 { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_num` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 25 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 25 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `seq_io::fasta::Record as FastaRecord` [INFO] [stdout] --> examples/step3b_read_fastq_seq_io.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use seq_io::fasta::Record as FastaRecord; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `seq_io::fastq::Record as FastqRecord` [INFO] [stdout] --> examples/step3b_read_fastq_seq_io.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use seq_io::fastq::Record as FastqRecord; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bioutils::references::ftp::download_grch38_primary_assembly_genome_fa_gz` [INFO] [stdout] --> examples/step3b_read_fastq_seq_io.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use bioutils::references::ftp::download_grch38_primary_assembly_genome_fa_gz; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `suffix_array::SuffixArray` [INFO] [stdout] --> examples/step3b_read_fastq_seq_io.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use suffix_array::SuffixArray; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fastq_ftp` [INFO] [stdout] --> examples/step3b_read_fastq_seq_io.rs:18:9 [INFO] [stdout] | [INFO] [stdout] 18 | let fastq_ftp = "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR170/009/SRR1700869/"; [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fastq_ftp` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fastq_gz` [INFO] [stdout] --> examples/step3b_read_fastq_seq_io.rs:19:9 [INFO] [stdout] | [INFO] [stdout] 19 | let fastq_gz = "SRR1700869.fastq.gz"; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fastq_gz` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reference_reader` [INFO] [stdout] --> examples/step3b_read_fastq_seq_io.rs:45:13 [INFO] [stdout] | [INFO] [stdout] 45 | let mut reference_reader = seq_io::fasta::Reader::new(reference); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reference_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fq_reader` [INFO] [stdout] --> examples/step3b_read_fastq_seq_io.rs:50:13 [INFO] [stdout] | [INFO] [stdout] 50 | let mut fq_reader = seq_io::fastq::Reader::new(fq); [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fq_reader` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> examples/step3b_read_fastq_seq_io.rs:45:9 [INFO] [stdout] | [INFO] [stdout] 45 | let mut reference_reader = seq_io::fasta::Reader::new(reference); [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] --> examples/step3b_read_fastq_seq_io.rs:50:9 [INFO] [stdout] | [INFO] [stdout] 50 | let mut fq_reader = seq_io::fastq::Reader::new(fq); [INFO] [stdout] | ----^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 10 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bioutils::utils::image::color::*` [INFO] [stdout] --> examples/quality_visual.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use bioutils::utils::image::color::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bioutils::charsets::quality::*` [INFO] [stdout] --> examples/quality_visual.rs:8:5 [INFO] [stdout] | [INFO] [stdout] 8 | use bioutils::charsets::quality::*; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ImageBuffer` [INFO] [stdout] --> examples/quality_visual.rs:12:13 [INFO] [stdout] | [INFO] [stdout] 12 | use image::{ImageBuffer, Rgb}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `seq_io::fasta::Record as FastaRecord` [INFO] [stdout] --> examples/step1_make_directories.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use seq_io::fasta::Record as FastaRecord; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `seq_io::fastq::Record as FastqRecord` [INFO] [stdout] --> examples/step1_make_directories.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use seq_io::fastq::Record as FastqRecord; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> examples/step1_make_directories.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bioutils::references::ftp::download_grch38_primary_assembly_genome_fa_gz` [INFO] [stdout] --> examples/step1_make_directories.rs:5:5 [INFO] [stdout] | [INFO] [stdout] 5 | use bioutils::references::ftp::download_grch38_primary_assembly_genome_fa_gz; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `suffix_array::SuffixArray` [INFO] [stdout] --> examples/step1_make_directories.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use suffix_array::SuffixArray; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fastq_ftp` [INFO] [stdout] --> examples/step1_make_directories.rs:15:9 [INFO] [stdout] | [INFO] [stdout] 15 | let fastq_ftp = "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR170/009/SRR1700869/"; [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fastq_ftp` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fastq_gz` [INFO] [stdout] --> examples/step1_make_directories.rs:16:9 [INFO] [stdout] | [INFO] [stdout] 16 | let fastq_gz = "SRR1700869.fastq.gz"; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fastq_gz` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reference_name` [INFO] [stdout] --> examples/step1_make_directories.rs:17:9 [INFO] [stdout] | [INFO] [stdout] 17 | let reference_name = "GRCh38.primary_assembly.genome.fa.gz"; [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reference_name` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fastq_file` [INFO] [stdout] --> examples/step1_make_directories.rs:18:9 [INFO] [stdout] | [INFO] [stdout] 18 | let fastq_file = &samples_directory.join("SRR1700869.fastq.gz"); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fastq_file` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `seq_io::fasta::Record as FastaRecord` [INFO] [stdout] --> examples/step2_download_files.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use seq_io::fasta::Record as FastaRecord; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `seq_io::fastq::Record as FastqRecord` [INFO] [stdout] --> examples/step2_download_files.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use seq_io::fastq::Record as FastqRecord; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::fs::File` [INFO] [stdout] --> examples/step2_download_files.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use std::fs::File; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `suffix_array::SuffixArray` [INFO] [stdout] --> examples/step2_download_files.rs:7:5 [INFO] [stdout] | [INFO] [stdout] 7 | use suffix_array::SuffixArray; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `bioutils::files::fastq::hash` [INFO] [stdout] --> examples/filter_paired_reads.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use bioutils::files::fastq::hash; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `seq_io::fastq::Record as FastqRecord` [INFO] [stdout] --> examples/filter_paired_reads.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use seq_io::fastq::Record as FastqRecord; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 9 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `reference_name` [INFO] [stdout] --> examples/step2_download_files.rs:20:9 [INFO] [stdout] | [INFO] [stdout] 20 | let reference_name = "GRCh38.primary_assembly.genome.fa.gz"; [INFO] [stdout] | ^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reference_name` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `fastq_file` [INFO] [stdout] --> examples/step2_download_files.rs:21:9 [INFO] [stdout] | [INFO] [stdout] 21 | let fastq_file = &samples_directory.join("SRR1700869.fastq.gz"); [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_fastq_file` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> examples/filter_paired_reads.rs:32:9 [INFO] [stdout] | [INFO] [stdout] 32 | let mut fq1_reader = seq_io::fastq::Reader::new(fq1); [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] --> examples/filter_paired_reads.rs:36:9 [INFO] [stdout] | [INFO] [stdout] 36 | let mut fq2_reader = seq_io::fastq::Reader::new(fq2); [INFO] [stdout] | ----^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 6 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `record_head` [INFO] [stdout] --> examples/align.rs:94:13 [INFO] [stdout] | [INFO] [stdout] 94 | let record_head = record.head(); [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_record_head` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `positions_forward` [INFO] [stdout] --> examples/align.rs:98:13 [INFO] [stdout] | [INFO] [stdout] 98 | let positions_forward = fastq_aligner(&mut fq_reader, sa); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_positions_forward` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `positions_reverse` [INFO] [stdout] --> examples/align.rs:104:13 [INFO] [stdout] | [INFO] [stdout] 104 | let positions_reverse = fastq_aligner(&mut fq_reader, sar); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_positions_reverse` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `positions` [INFO] [stdout] --> examples/align.rs:122:13 [INFO] [stdout] | [INFO] [stdout] 122 | let positions = sa.search_all(seq); [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_positions` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sa` [INFO] [stdout] --> examples/align.rs:111:67 [INFO] [stdout] | [INFO] [stdout] 111 | pub fn fastq_aligner(fq_reader: &mut seq_io::fastq::Reader, sa: SuffixArray) [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_sa` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 5 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 33.64s [INFO] running `Command { std: "docker" "inspect" "32cca7dae4f10c168544abd10249f7a493332f7ca32c02197259950355a2e6c7", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "32cca7dae4f10c168544abd10249f7a493332f7ca32c02197259950355a2e6c7", kill_on_drop: false }` [INFO] [stdout] 32cca7dae4f10c168544abd10249f7a493332f7ca32c02197259950355a2e6c7