[INFO] cloning repository https://github.com/Jakeelamb/Raptor
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Jakeelamb/Raptor" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJakeelamb%2FRaptor", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJakeelamb%2FRaptor'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 1ef0b3fc7f0d3fcb9aec9bba0091f5c65dc16ffb
[INFO] checking Jakeelamb/Raptor against master#1210e9fa3ee9c9712fa694f90f7a032f2f0fd786 for feb-17
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJakeelamb%2FRaptor" "/workspace/builds/worker-5-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/Jakeelamb/Raptor
[INFO] finished tweaking git repo https://github.com/Jakeelamb/Raptor
[INFO] tweaked toml for git repo https://github.com/Jakeelamb/Raptor written to /workspace/builds/worker-5-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/Jakeelamb/Raptor on toolchain 1210e9fa3ee9c9712fa694f90f7a032f2f0fd786
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1210e9fa3ee9c9712fa694f90f7a032f2f0fd786" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/Jakeelamb/Raptor 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" "+1210e9fa3ee9c9712fa694f90f7a032f2f0fd786" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:61361fe0aef631f17e9d025a70c5a647956f8c671dd02950a60ad3f5cc5526d7" "/opt/rustwide/cargo-home/bin/cargo" "+1210e9fa3ee9c9712fa694f90f7a032f2f0fd786" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] b7b9a34ed4edf004da2da8b893dbc2433f2bc275b4de41fd091c782f9207d852
[INFO] running `Command { std: "docker" "start" "-a" "b7b9a34ed4edf004da2da8b893dbc2433f2bc275b4de41fd091c782f9207d852", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "b7b9a34ed4edf004da2da8b893dbc2433f2bc275b4de41fd091c782f9207d852", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "b7b9a34ed4edf004da2da8b893dbc2433f2bc275b4de41fd091c782f9207d852", kill_on_drop: false }`
[INFO] [stdout] b7b9a34ed4edf004da2da8b893dbc2433f2bc275b4de41fd091c782f9207d852
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:61361fe0aef631f17e9d025a70c5a647956f8c671dd02950a60ad3f5cc5526d7" "/opt/rustwide/cargo-home/bin/cargo" "+1210e9fa3ee9c9712fa694f90f7a032f2f0fd786" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "start" "-a" "57af033fca11891a7168c4f5818067ab9a6c4eacc49c15b123e655d81ef8ba83", kill_on_drop: false }`
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[INFO] [stdout] warning: use of deprecated function `graph::isoform_filter::edit_distance`: Use kmer_jaccard_similarity for 100-1000x speedup
[INFO] [stdout]    --> src/graph/isoform_filter.rs:365:20
[INFO] [stdout]     |
[INFO] [stdout] 365 |         assert_eq!(edit_distance("GATTACA", "GCTTACA"), 1);
[INFO] [stdout]     |                    ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `graph::isoform_filter::edit_distance`: Use kmer_jaccard_similarity for 100-1000x speedup
[INFO] [stdout]    --> src/graph/isoform_filter.rs:366:20
[INFO] [stdout]     |
[INFO] [stdout] 366 |         assert_eq!(edit_distance("GATTACA", "GATTACA"), 0);
[INFO] [stdout]     |                    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `graph::isoform_filter::edit_distance`: Use kmer_jaccard_similarity for 100-1000x speedup
[INFO] [stdout]    --> src/graph/isoform_filter.rs:367:20
[INFO] [stdout]     |
[INFO] [stdout] 367 |         assert_eq!(edit_distance("GATTACA", "GATT"), 3);
[INFO] [stdout]     |                    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `h1`
[INFO] [stdout]    --> src/kmer/nthash.rs:325:13
[INFO] [stdout]     |
[INFO] [stdout] 325 |         let h1 = nthash(b"AAAAAAAA").unwrap();
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_h1`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `h2`
[INFO] [stdout]    --> src/kmer/nthash.rs:326:13
[INFO] [stdout]     |
[INFO] [stdout] 326 |         let h2 = nthash(b"CCCCCCCC").unwrap();
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_h2`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `h3`
[INFO] [stdout]    --> src/kmer/nthash.rs:327:13
[INFO] [stdout]     |
[INFO] [stdout] 327 |         let h3 = nthash(b"ACGTACGT").unwrap();
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_h3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `h4`
[INFO] [stdout]    --> src/kmer/nthash.rs:328:13
[INFO] [stdout]     |
[INFO] [stdout] 328 |         let h4 = nthash(b"GTACGTAC").unwrap();
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_h4`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: comparison is useless due to type limits
[INFO] [stdout]    --> src/accel/cpu_backend.rs:439:17
[INFO] [stdout]     |
[INFO] [stdout] 439 |         assert!(overlaps.len() >= 0); // Just verify it runs without error
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_comparisons)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `raptor::kmer::kmer::canonical_kmer`: Use KmerU64::canonical() for 6x memory reduction
[INFO] [stdout]  --> tests/greedy.rs:3:26
[INFO] [stdout]   |
[INFO] [stdout] 3 | use raptor::kmer::kmer::{canonical_kmer, decode_kmer};
[INFO] [stdout]   |                          ^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `self`
[INFO] [stdout]  --> examples/traverse_paths.rs:4:15
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::io::{self, BufWriter, Write};
[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: `ahash::AHashMap`
[INFO] [stdout]  --> benches/kmer_counting.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use ahash::AHashMap;
[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: `i`
[INFO] [stdout]   --> examples/traverse_paths.rs:91:14
[INFO] [stdout]    |
[INFO] [stdout] 91 |         for (i, (seg_id, orientation)) in path.iter().enumerate() {
[INFO] [stdout]    |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `n`
[INFO] [stdout]   --> benches/isoform_paths.rs:79:18
[INFO] [stdout]    |
[INFO] [stdout] 79 |             |b, &n| {
[INFO] [stdout]    |                  ^ help: if this is intentional, prefix it with an underscore: `_n`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `generate_sequence` is never used
[INFO] [stdout]  --> benches/isoform_paths.rs:7:4
[INFO] [stdout]   |
[INFO] [stdout] 7 | fn generate_sequence(len: usize) -> String {
[INFO] [stdout]   |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `graph::isoform_filter::edit_distance`: Use kmer_jaccard_similarity for 100-1000x speedup
[INFO] [stdout]    --> src/graph/isoform_filter.rs:365:20
[INFO] [stdout]     |
[INFO] [stdout] 365 |         assert_eq!(edit_distance("GATTACA", "GCTTACA"), 1);
[INFO] [stdout]     |                    ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `graph::isoform_filter::edit_distance`: Use kmer_jaccard_similarity for 100-1000x speedup
[INFO] [stdout]    --> src/graph/isoform_filter.rs:366:20
[INFO] [stdout]     |
[INFO] [stdout] 366 |         assert_eq!(edit_distance("GATTACA", "GATTACA"), 0);
[INFO] [stdout]     |                    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `graph::isoform_filter::edit_distance`: Use kmer_jaccard_similarity for 100-1000x speedup
[INFO] [stdout]    --> src/graph/isoform_filter.rs:367:20
[INFO] [stdout]     |
[INFO] [stdout] 367 |         assert_eq!(edit_distance("GATTACA", "GATT"), 3);
[INFO] [stdout]     |                    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `h1`
[INFO] [stdout]    --> src/kmer/nthash.rs:325:13
[INFO] [stdout]     |
[INFO] [stdout] 325 |         let h1 = nthash(b"AAAAAAAA").unwrap();
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_h1`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `h2`
[INFO] [stdout]    --> src/kmer/nthash.rs:326:13
[INFO] [stdout]     |
[INFO] [stdout] 326 |         let h2 = nthash(b"CCCCCCCC").unwrap();
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_h2`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `h3`
[INFO] [stdout]    --> src/kmer/nthash.rs:327:13
[INFO] [stdout]     |
[INFO] [stdout] 327 |         let h3 = nthash(b"ACGTACGT").unwrap();
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_h3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `h4`
[INFO] [stdout]    --> src/kmer/nthash.rs:328:13
[INFO] [stdout]     |
[INFO] [stdout] 328 |         let h4 = nthash(b"GTACGTAC").unwrap();
[INFO] [stdout]     |             ^^ help: if this is intentional, prefix it with an underscore: `_h4`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: comparison is useless due to type limits
[INFO] [stdout]    --> src/accel/cpu_backend.rs:439:17
[INFO] [stdout]     |
[INFO] [stdout] 439 |         assert!(overlaps.len() >= 0); // Just verify it runs without error
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_comparisons)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 10s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "57af033fca11891a7168c4f5818067ab9a6c4eacc49c15b123e655d81ef8ba83", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "57af033fca11891a7168c4f5818067ab9a6c4eacc49c15b123e655d81ef8ba83", kill_on_drop: false }`
[INFO] [stdout] 57af033fca11891a7168c4f5818067ab9a6c4eacc49c15b123e655d81ef8ba83
