[INFO] cloning repository https://github.com/Archina/BioInformatics-3
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Archina/BioInformatics-3" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FArchina%2FBioInformatics-3", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FArchina%2FBioInformatics-3'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 87b67b3e19242d30970132e85d61545c6c9779d1
[INFO] checking Archina/BioInformatics-3 against try#a7a572ce3edd6d476191fbfe92c9c1986e009b34 for pr-87190-3
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FArchina%2FBioInformatics-3" "/workspace/builds/worker-7/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/Archina/BioInformatics-3 on toolchain a7a572ce3edd6d476191fbfe92c9c1986e009b34
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/Archina/BioInformatics-3
[INFO] finished tweaking git repo https://github.com/Archina/BioInformatics-3
[INFO] tweaked toml for git repo https://github.com/Archina/BioInformatics-3 written to /workspace/builds/worker-7/source/Cargo.toml
[INFO] crate git repo https://github.com/Archina/BioInformatics-3 already has a lockfile, it will not be regenerated
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 1851d7c60321770f423734d741b305c0967b008c8634f8b2cc708a3921957f37
[INFO] running `Command { std: "docker" "start" "-a" "1851d7c60321770f423734d741b305c0967b008c8634f8b2cc708a3921957f37", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "1851d7c60321770f423734d741b305c0967b008c8634f8b2cc708a3921957f37", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1851d7c60321770f423734d741b305c0967b008c8634f8b2cc708a3921957f37", kill_on_drop: false }`
[INFO] [stdout] 1851d7c60321770f423734d741b305c0967b008c8634f8b2cc708a3921957f37
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+a7a572ce3edd6d476191fbfe92c9c1986e009b34" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] de15a7c85de1700702f243304e12800c6c287d91d8009deb0040d0917f1e8bbc
[INFO] running `Command { std: "docker" "start" "-a" "de15a7c85de1700702f243304e12800c6c287d91d8009deb0040d0917f1e8bbc", kill_on_drop: false }`
[INFO] [stderr] Copying to /tmp/fixit
[INFO] [stderr] Running `cargo fix --edition`
[INFO] [stderr]     Checking prog_03 v0.1.0 (/tmp/fixit)
[INFO] [stderr]    Migrating src/main.rs from 2018 edition to 2021
[INFO] [stderr]        Fixed src/main.rs (1 fix)
[INFO] [stderr]        Fixed src/sequences.rs (2 fixes)
[INFO] [stderr]        Fixed src/matrix.rs (1 fix)
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 0.77s
[INFO] [stderr] Running `cargo check` to verify 2021
[INFO] [stderr]     Checking prog_03 v0.1.0 (/tmp/fixit)
[INFO] [stdout] error[E0425]: cannot find function `from_file` in this scope
[INFO] [stdout]    --> src/sequences.rs:134:25
[INFO] [stdout]     |
[INFO] [stdout] 134 |         let sequences = from_file(Path::new("data/align4.fasta"));
[INFO] [stdout]     |                         ^^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this function
[INFO] [stdout]     |
[INFO] [stdout] 133 |     use crate::sequences::from_file;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Path`
[INFO] [stdout]    --> src/sequences.rs:134:35
[INFO] [stdout]     |
[INFO] [stdout] 134 |         let sequences = from_file(Path::new("data/align4.fasta"));
[INFO] [stdout]     |                                   ^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing one of these items
[INFO] [stdout]     |
[INFO] [stdout] 133 |     use crate::Path;
[INFO] [stdout]     |
[INFO] [stdout] 133 |     use std::path::Path;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0422]: cannot find struct, variant or union type `Sequence` in this scope
[INFO] [stdout]    --> src/sequences.rs:143:21
[INFO] [stdout]     |
[INFO] [stdout] 143 |         let seq_a = Sequence{
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 133 |     use crate::sequences::Sequence;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0422]: cannot find struct, variant or union type `Sequence` in this scope
[INFO] [stdout]    --> src/sequences.rs:147:21
[INFO] [stdout]     |
[INFO] [stdout] 147 |         let seq_b = Sequence{
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 133 |     use crate::sequences::Sequence;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0422]: cannot find struct, variant or union type `Sequence` in this scope
[INFO] [stdout]    --> src/sequences.rs:171:21
[INFO] [stdout]     |
[INFO] [stdout] 171 |         let seq_a = Sequence{
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 133 |     use crate::sequences::Sequence;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0422]: cannot find struct, variant or union type `Sequence` in this scope
[INFO] [stdout]    --> src/sequences.rs:175:21
[INFO] [stdout]     |
[INFO] [stdout] 175 |         let seq_b = Sequence{
[INFO] [stdout]     |                     ^^^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 133 |     use crate::sequences::Sequence;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Matrix`
[INFO] [stdout]    --> src/matrix.rs:100:26
[INFO] [stdout]     |
[INFO] [stdout] 100 |         let mut matrix = Matrix::<f64>::new(11, 10, 8184.0);
[INFO] [stdout]     |                          ^^^^^^ not found in this scope
[INFO] [stdout]     |
[INFO] [stdout] help: consider importing this struct
[INFO] [stdout]     |
[INFO] [stdout] 99  |     use crate::matrix::Matrix;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 7 previous errors
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0422, E0425, E0433.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0422`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `prog_03` due to 8 previous errors
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] [stderr] error: build failed
[INFO] [stderr] error: failed to check after updating to 2021
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   process didn't exit successfully: `cargo check --frozen --all --all-targets --message-format=json` (exit status: 101)
[INFO] running `Command { std: "docker" "inspect" "de15a7c85de1700702f243304e12800c6c287d91d8009deb0040d0917f1e8bbc", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "de15a7c85de1700702f243304e12800c6c287d91d8009deb0040d0917f1e8bbc", kill_on_drop: false }`
[INFO] [stdout] de15a7c85de1700702f243304e12800c6c287d91d8009deb0040d0917f1e8bbc