[INFO] cloning repository https://github.com/HopedWall/rs-vgaligner [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/HopedWall/rs-vgaligner" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2Frs-vgaligner", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2Frs-vgaligner'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 557d27d9da0a035af42de9bd60c8c1e62cc1a64b [INFO] checking HopedWall/rs-vgaligner against try#a7a572ce3edd6d476191fbfe92c9c1986e009b34 for pr-87190-3 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2Frs-vgaligner" "/workspace/builds/worker-94/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-94/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/HopedWall/rs-vgaligner 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/HopedWall/rs-vgaligner [INFO] finished tweaking git repo https://github.com/HopedWall/rs-vgaligner [INFO] tweaked toml for git repo https://github.com/HopedWall/rs-vgaligner written to /workspace/builds/worker-94/source/Cargo.toml [INFO] crate git repo https://github.com/HopedWall/rs-vgaligner 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] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded float-cmp v0.9.0 [INFO] [stderr] Downloaded serde_with_macros v1.4.1 [INFO] [stderr] Downloaded bio v0.32.0 [INFO] [stderr] Downloaded serde_with v1.8.1 [INFO] [stderr] Downloaded handlegraph v0.5.0 [INFO] [stderr] Downloaded gfa v0.8.0 [INFO] [stderr] Downloaded newtype_derive v0.1.4 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/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] 25266868aaba00ff44b6003eaf6aa9871efa295073bfc34832e0bca69d57e2ce [INFO] running `Command { std: "docker" "start" "-a" "25266868aaba00ff44b6003eaf6aa9871efa295073bfc34832e0bca69d57e2ce", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "25266868aaba00ff44b6003eaf6aa9871efa295073bfc34832e0bca69d57e2ce", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "25266868aaba00ff44b6003eaf6aa9871efa295073bfc34832e0bca69d57e2ce", kill_on_drop: false }` [INFO] [stdout] 25266868aaba00ff44b6003eaf6aa9871efa295073bfc34832e0bca69d57e2ce [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/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] 60d663a22649eb649d7ca2d4d01ebafc81c6a2adceed24ab648c85f60ed8514b [INFO] running `Command { std: "docker" "start" "-a" "60d663a22649eb649d7ca2d4d01ebafc81c6a2adceed24ab648c85f60ed8514b", kill_on_drop: false }` [INFO] [stderr] Copying to /tmp/fixit [INFO] [stderr] Running `cargo fix --edition` [INFO] [stderr] Compiling syn v1.0.60 [INFO] [stderr] Compiling libc v0.2.86 [INFO] [stderr] Compiling serde_derive v1.0.125 [INFO] [stderr] Compiling serde v1.0.125 [INFO] [stderr] Compiling ryu v1.0.5 [INFO] [stderr] Checking byteorder v1.4.2 [INFO] [stderr] Checking once_cell v1.7.0 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Checking itoa v0.4.7 [INFO] [stderr] Checking regex-syntax v0.6.22 [INFO] [stderr] Compiling rayon-core v1.9.0 [INFO] [stderr] Checking hashbrown v0.9.1 [INFO] [stderr] Compiling fnv v1.0.7 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Compiling strsim v0.10.0 [INFO] [stderr] Compiling lexical-core v0.7.5 [INFO] [stderr] Compiling ident_case v1.0.1 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] 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darling_macro v0.12.4 [INFO] [stderr] Checking enum-map v0.6.4 [INFO] [stderr] Checking bytemuck v1.5.1 [INFO] [stderr] Compiling darling v0.12.4 [INFO] [stderr] Compiling serde_with_macros v1.4.1 [INFO] [stderr] Checking thiserror v1.0.26 [INFO] [stderr] Checking bio-types v0.12.0 [INFO] [stderr] Checking snafu v0.6.10 [INFO] [stderr] Checking bstr v0.2.15 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking multimap v0.8.2 [INFO] [stderr] Checking boomphf v0.5.9 [INFO] [stderr] Checking bincode v1.3.3 [INFO] [stderr] Checking serde_with v1.8.1 [INFO] [stderr] Checking clap v2.33.3 [INFO] [stderr] Checking csv v1.1.5 [INFO] [stderr] Checking gfa v0.8.0 [INFO] [stderr] Checking handlegraph v0.5.0 [INFO] [stderr] Checking vgaligner v0.1.0 (/tmp/fixit) [INFO] [stderr] Migrating src/main.rs from 2018 edition to 2021 [INFO] [stderr] Fixed src/index.rs (9 fixes) [INFO] [stderr] Fixed src/map.rs (7 fixes) [INFO] [stderr] Fixed src/subcommands/index_main.rs (1 fix) [INFO] [stderr] Fixed src/kmer.rs (3 fixes) [INFO] [stderr] Fixed src/chain.rs (11 fixes) [INFO] [stderr] Fixed src/io.rs (4 fixes) [INFO] [stderr] Fixed src/subcommands/map_main.rs (4 fixes) [INFO] [stderr] Fixed src/serialization.rs (1 fix) [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `GFAParser` [INFO] [stdout] --> src/map.rs:93:22 [INFO] [stdout] | [INFO] [stdout] 93 | let parser = GFAParser::new(); [INFO] [stdout] | ^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing one of these items [INFO] [stdout] | [INFO] [stdout] 92 | use crate::chain::test::GFAParser; [INFO] [stdout] | [INFO] [stdout] 92 | use gfa::parser::GFAParser; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `GFA` in this scope [INFO] [stdout] --> src/map.rs:94:18 [INFO] [stdout] | [INFO] [stdout] 94 | let gfa: GFA = parser.parse_file(&PathBuf::from("./test/test.gfa")).unwrap(); [INFO] [stdout] | ^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing one of these items [INFO] [stdout] | [INFO] [stdout] 92 | use crate::chain::test::GFA; [INFO] [stdout] | [INFO] [stdout] 92 | use gfa::gfa::GFA; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `PathBuf` [INFO] [stdout] --> src/map.rs:94:54 [INFO] [stdout] | [INFO] [stdout] 94 | let gfa: GFA = parser.parse_file(&PathBuf::from("./test/test.gfa")).unwrap(); [INFO] [stdout] | ^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing one of these items [INFO] [stdout] | [INFO] [stdout] 92 | use crate::chain::test::PathBuf; [INFO] [stdout] | [INFO] [stdout] 92 | use std::path::PathBuf; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `HashGraph` [INFO] [stdout] --> src/map.rs:95:21 [INFO] [stdout] | [INFO] [stdout] 95 | let graph = HashGraph::from_gfa(&gfa); [INFO] [stdout] | ^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing one of these items [INFO] [stdout] | [INFO] [stdout] 92 | use crate::chain::test::HashGraph; [INFO] [stdout] | [INFO] [stdout] 92 | use handlegraph::hashgraph::HashGraph; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0433]: failed to resolve: use of undeclared type `Index` [INFO] [stdout] --> src/map.rs:97:21 [INFO] [stdout] | [INFO] [stdout] 97 | let index = Index::build(&graph, 11, 100, [INFO] [stdout] | ^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing one of these items [INFO] [stdout] | [INFO] [stdout] 92 | use bio::io::fasta::Index; [INFO] [stdout] | [INFO] [stdout] 92 | use core::ops::Index; [INFO] [stdout] | [INFO] [stdout] 92 | use crate::map::Index; [INFO] [stdout] | [INFO] [stdout] 92 | use serde_json::value::Index; [INFO] [stdout] | [INFO] [stdout] and 1 other candidate [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `read_seqs_from_file` in this scope [INFO] [stdout] --> src/map.rs:99:21 [INFO] [stdout] | [INFO] [stdout] 99 | let query = read_seqs_from_file("./test/test.fa").unwrap(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing this function [INFO] [stdout] | [INFO] [stdout] 92 | use crate::io::read_seqs_from_file; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `map_reads` in this scope [INFO] [stdout] --> src/map.rs:101:9 [INFO] [stdout] | [INFO] [stdout] 101 | map_reads(&index, &query,50, 1000, [INFO] [stdout] | ^^^^^^^^^ not found in this scope [INFO] [stdout] | [INFO] [stdout] help: consider importing this function [INFO] [stdout] | [INFO] [stdout] 92 | use crate::map::map_reads; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `handlegraph::handle::Handle` [INFO] [stdout] --> src/index.rs:423:9 [INFO] [stdout] | [INFO] [stdout] 423 | use handlegraph::handle::Handle; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `anchor_id` should have an upper camel case name [INFO] [stdout] --> src/chain.rs:18:6 [INFO] [stdout] | [INFO] [stdout] 18 | type anchor_id = u64; [INFO] [stdout] | ^^^^^^^^^ help: convert the identifier to upper camel case: `AnchorId` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `anchor_id` should have an upper camel case name [INFO] [stdout] --> src/chain.rs:18:6 [INFO] [stdout] | [INFO] [stdout] 18 | type anchor_id = u64; [INFO] [stdout] | ^^^^^^^^^ help: convert the identifier to upper camel case: `AnchorId` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/io.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 7 previous errors; 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0412, E0425, E0433. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0412`. [INFO] [stdout] [INFO] [stderr] error: could not compile `vgaligner` due to 8 previous errors; 3 warnings emitted [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/io.rs:9:5 [INFO] [stdout] | [INFO] [stdout] 9 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `score` is never read [INFO] [stdout] --> src/chain.rs:185:13 [INFO] [stdout] | [INFO] [stdout] 185 | let mut score : f64 = a.max_chain_score; [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_assignments)]` on by default [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function is never used: `extract_query_subsequence` [INFO] [stdout] --> src/chain.rs:432:8 [INFO] [stdout] | [INFO] [stdout] 432 | pub fn extract_query_subsequence(index : &Index, chains : &Vec, _query : &InputSequence) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: build failed [INFO] [stderr] error: failed to migrate to next edition [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `cargo fix --edition --allow-no-vcs --allow-dirty --frozen --all --all-targets --message-format=json` (exit status: 101) [INFO] running `Command { std: "docker" "inspect" "60d663a22649eb649d7ca2d4d01ebafc81c6a2adceed24ab648c85f60ed8514b", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "60d663a22649eb649d7ca2d4d01ebafc81c6a2adceed24ab648c85f60ed8514b", kill_on_drop: false }` [INFO] [stdout] 60d663a22649eb649d7ca2d4d01ebafc81c6a2adceed24ab648c85f60ed8514b