[INFO] fetching crate cytos 1.2.1...
[INFO] testing cytos-1.2.1 against beta-2025-09-21 for beta-1.91-3
[INFO] extracting crate cytos 1.2.1 into /workspace/builds/worker-0-tc2/source
[INFO] started tweaking crates.io crate cytos 1.2.1
[INFO] finished tweaking crates.io crate cytos 1.2.1
[INFO] tweaked toml for crates.io crate cytos 1.2.1 written to /workspace/builds/worker-0-tc2/source/Cargo.toml
[INFO] validating manifest of crates.io crate cytos 1.2.1 on toolchain beta-2025-09-21
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2025-09-21" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate cytos 1.2.1 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" "+beta-2025-09-21" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] c895a96ea10fa9e34163f39e225a76d9c77faa396eb6a454ef5b42c0e902a2a1
[INFO] running `Command { std: "docker" "start" "-a" "c895a96ea10fa9e34163f39e225a76d9c77faa396eb6a454ef5b42c0e902a2a1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "c895a96ea10fa9e34163f39e225a76d9c77faa396eb6a454ef5b42c0e902a2a1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c895a96ea10fa9e34163f39e225a76d9c77faa396eb6a454ef5b42c0e902a2a1", kill_on_drop: false }`
[INFO] [stdout] c895a96ea10fa9e34163f39e225a76d9c77faa396eb6a454ef5b42c0e902a2a1
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 168dba1daf877124ff89355de9b8fb7193ade2d92372f642a325f83f5b54fc2e
[INFO] running `Command { std: "docker" "start" "-a" "168dba1daf877124ff89355de9b8fb7193ade2d92372f642a325f83f5b54fc2e", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.150
[INFO] [stderr]    Compiling memchr v2.6.4
[INFO] [stderr]    Compiling num-traits v0.2.17
[INFO] [stderr]    Compiling num-integer v0.1.45
[INFO] [stderr]    Compiling serde v1.0.192
[INFO] [stderr]    Compiling matrixmultiply v0.3.8
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling bytemuck v1.14.0
[INFO] [stderr]    Compiling num-rational v0.4.1
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling rustversion v1.0.14
[INFO] [stderr]    Compiling safe_arch v0.7.1
[INFO] [stderr]    Compiling regex-syntax v0.8.2
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling aho-corasick v1.1.2
[INFO] [stderr]    Compiling wide v0.7.13
[INFO] [stderr]    Compiling getrandom v0.2.11
[INFO] [stderr]    Compiling rand_core v0.6.4
[INFO] [stderr]    Compiling rand_chacha v0.3.1
[INFO] [stderr]    Compiling num-complex v0.4.4
[INFO] [stderr]    Compiling rand v0.8.5
[INFO] [stderr]    Compiling approx v0.5.1
[INFO] [stderr]    Compiling thiserror v1.0.50
[INFO] [stderr]    Compiling rustix v0.38.24
[INFO] [stderr]    Compiling anstyle-parse v0.2.2
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling regex-automata v0.4.3
[INFO] [stderr]    Compiling rand_distr v0.4.3
[INFO] [stderr]    Compiling simba v0.6.0
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling thiserror-impl v1.0.50
[INFO] [stderr]    Compiling hashbrown v0.14.2
[INFO] [stderr]    Compiling anstyle-query v1.0.0
[INFO] [stderr]    Compiling bitflags v2.4.1
[INFO] [stderr]    Compiling anyhow v1.0.75
[INFO] [stderr]    Compiling linux-raw-sys v0.4.11
[INFO] [stderr]    Compiling indexmap v2.1.0
[INFO] [stderr]    Compiling anstream v0.6.4
[INFO] [stderr]    Compiling strum_macros v0.25.3
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling enum-map-derive v0.6.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling csv-core v0.1.11
[INFO] [stderr]    Compiling bit-vec v0.6.3
[INFO] [stderr]    Compiling fixedbitset v0.4.2
[INFO] [stderr]    Compiling either v1.9.0
[INFO] [stderr]    Compiling ryu v1.0.15
[INFO] [stderr]    Compiling itoa v1.0.9
[INFO] [stderr]    Compiling bit-set v0.5.3
[INFO] [stderr]    Compiling itertools v0.11.0
[INFO] [stderr]    Compiling petgraph v0.6.4
[INFO] [stderr]    Compiling csv v1.3.0
[INFO] [stderr]    Compiling clap_builder v4.4.8
[INFO] [stderr]    Compiling regex v1.10.2
[INFO] [stderr]    Compiling is-terminal v0.4.9
[INFO] [stderr]    Compiling enum-map v1.1.1
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling bv v0.11.1
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]    Compiling bio-types v1.0.1
[INFO] [stderr]    Compiling multimap v0.8.3
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling ndarray v0.15.6
[INFO] [stderr]    Compiling itertools-num v0.1.3
[INFO] [stderr]    Compiling ordered-float v3.9.2
[INFO] [stderr]    Compiling clap_derive v4.4.7
[INFO] [stderr]    Compiling bytecount v0.6.7
[INFO] [stderr]    Compiling strum v0.25.0
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling iana-time-zone v0.1.58
[INFO] [stderr]    Compiling editdistancek v1.0.2
[INFO] [stderr]    Compiling log v0.4.20
[INFO] [stderr]    Compiling termcolor v1.4.0
[INFO] [stderr]    Compiling triple_accel v0.4.0
[INFO] [stderr]    Compiling chrono v0.4.31
[INFO] [stderr]    Compiling env_logger v0.10.1
[INFO] [stderr]    Compiling clap v4.4.8
[INFO] [stderr]    Compiling nalgebra v0.29.0
[INFO] [stderr]    Compiling statrs v0.16.0
[INFO] [stderr]    Compiling bio v1.4.0
[INFO] [stderr]    Compiling cytos v1.2.1 (/opt/rustwide/workdir)
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]   --> src/cli/msa/concat.rs:25:28
[INFO] [stdout]    |
[INFO] [stdout] 25 | fn read_fasta_files(input: &Vec<PathBuf>) -> CytosResult<HashMap<&PathBuf, FastaFile>> {
[INFO] [stdout]    |                            ^^^^^^^^^^^^^                         ^^^^^^^^  ^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]    |                            |                                     |
[INFO] [stdout]    |                            |                                     the same lifetime is elided here
[INFO] [stdout]    |                            the lifetime is elided here
[INFO] [stdout]    |
[INFO] [stdout]    = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout]    = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]    |
[INFO] [stdout] 25 | fn read_fasta_files(input: &Vec<PathBuf>) -> CytosResult<HashMap<&PathBuf, FastaFile<'_>>> {
[INFO] [stdout]    |                                                                                     ++++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's named elsewhere is confusing
[INFO] [stdout]   --> src/model/fasta/fasta_file.rs:17:57
[INFO] [stdout]    |
[INFO] [stdout] 17 |     pub fn load(path: &'a path::PathBuf) -> CytosResult<FastaFile> {
[INFO] [stdout]    |                        -- the lifetime is named here    ^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]    |
[INFO] [stdout]    = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: consistently use `'a`
[INFO] [stdout]    |
[INFO] [stdout] 17 |     pub fn load(path: &'a path::PathBuf) -> CytosResult<FastaFile<'a>> {
[INFO] [stdout]    |                                                                  ++++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 24s
[INFO] running `Command { std: "docker" "inspect" "168dba1daf877124ff89355de9b8fb7193ade2d92372f642a325f83f5b54fc2e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "168dba1daf877124ff89355de9b8fb7193ade2d92372f642a325f83f5b54fc2e", kill_on_drop: false }`
[INFO] [stdout] 168dba1daf877124ff89355de9b8fb7193ade2d92372f642a325f83f5b54fc2e
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] fc160f6f8051d8add84811ac60917e053a62c3fb1d8d173a626b97e62d7173dd
[INFO] running `Command { std: "docker" "start" "-a" "fc160f6f8051d8add84811ac60917e053a62c3fb1d8d173a626b97e62d7173dd", kill_on_drop: false }`
[INFO] [stderr]    Compiling cytos v1.2.1 (/opt/rustwide/workdir)
[INFO] [stdout] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stdout]   --> src/cli/msa/concat.rs:25:28
[INFO] [stdout]    |
[INFO] [stdout] 25 | fn read_fasta_files(input: &Vec<PathBuf>) -> CytosResult<HashMap<&PathBuf, FastaFile>> {
[INFO] [stdout]    |                            ^^^^^^^^^^^^^                         ^^^^^^^^  ^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]    |                            |                                     |
[INFO] [stdout]    |                            |                                     the same lifetime is elided here
[INFO] [stdout]    |                            the lifetime is elided here
[INFO] [stdout]    |
[INFO] [stdout]    = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout]    = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default
[INFO] [stdout] help: use `'_` for type paths
[INFO] [stdout]    |
[INFO] [stdout] 25 | fn read_fasta_files(input: &Vec<PathBuf>) -> CytosResult<HashMap<&PathBuf, FastaFile<'_>>> {
[INFO] [stdout]    |                                                                                     ++++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: hiding a lifetime that's named elsewhere is confusing
[INFO] [stdout]   --> src/model/fasta/fasta_file.rs:17:57
[INFO] [stdout]    |
[INFO] [stdout] 17 |     pub fn load(path: &'a path::PathBuf) -> CytosResult<FastaFile> {
[INFO] [stdout]    |                        -- the lifetime is named here    ^^^^^^^^^ the same lifetime is hidden here
[INFO] [stdout]    |
[INFO] [stdout]    = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stdout] help: consistently use `'a`
[INFO] [stdout]    |
[INFO] [stdout] 17 |     pub fn load(path: &'a path::PathBuf) -> CytosResult<FastaFile<'a>> {
[INFO] [stdout]    |                                                                  ++++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.84s
[INFO] running `Command { std: "docker" "inspect" "fc160f6f8051d8add84811ac60917e053a62c3fb1d8d173a626b97e62d7173dd", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "fc160f6f8051d8add84811ac60917e053a62c3fb1d8d173a626b97e62d7173dd", kill_on_drop: false }`
[INFO] [stdout] fc160f6f8051d8add84811ac60917e053a62c3fb1d8d173a626b97e62d7173dd
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 3fbfe202d245b8eb6c2a398eeb827674c1c66aad642c44ccd85c887348baa44a
[INFO] running `Command { std: "docker" "start" "-a" "3fbfe202d245b8eb6c2a398eeb827674c1c66aad642c44ccd85c887348baa44a", kill_on_drop: false }`
[INFO] [stderr] warning: hiding a lifetime that's elided elsewhere is confusing
[INFO] [stderr]   --> src/cli/msa/concat.rs:25:28
[INFO] [stderr]    |
[INFO] [stderr] 25 | fn read_fasta_files(input: &Vec<PathBuf>) -> CytosResult<HashMap<&PathBuf, FastaFile>> {
[INFO] [stderr]    |                            ^^^^^^^^^^^^^                         ^^^^^^^^  ^^^^^^^^^ the same lifetime is hidden here
[INFO] [stderr]    |                            |                                     |
[INFO] [stderr]    |                            |                                     the same lifetime is elided here
[INFO] [stderr]    |                            the lifetime is elided here
[INFO] [stderr]    |
[INFO] [stderr]    = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stderr]    = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default
[INFO] [stderr] help: use `'_` for type paths
[INFO] [stderr]    |
[INFO] [stderr] 25 | fn read_fasta_files(input: &Vec<PathBuf>) -> CytosResult<HashMap<&PathBuf, FastaFile<'_>>> {
[INFO] [stderr]    |                                                                                     ++++
[INFO] [stderr] 
[INFO] [stderr] warning: hiding a lifetime that's named elsewhere is confusing
[INFO] [stderr]   --> src/model/fasta/fasta_file.rs:17:57
[INFO] [stderr]    |
[INFO] [stderr] 17 |     pub fn load(path: &'a path::PathBuf) -> CytosResult<FastaFile> {
[INFO] [stderr]    |                        -- the lifetime is named here    ^^^^^^^^^ the same lifetime is hidden here
[INFO] [stderr]    |
[INFO] [stderr]    = help: the same lifetime is referred to in inconsistent ways, making the signature confusing
[INFO] [stderr] help: consistently use `'a`
[INFO] [stderr]    |
[INFO] [stderr] 17 |     pub fn load(path: &'a path::PathBuf) -> CytosResult<FastaFile<'a>> {
[INFO] [stderr]    |                                                                  ++++
[INFO] [stderr] 
[INFO] [stderr] warning: `cytos` (bin "cytos" test) generated 2 warnings (run `cargo fix --bin "cytos" --tests` to apply 2 suggestions)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.14s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/cytos-f743f11d67843a19)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "3fbfe202d245b8eb6c2a398eeb827674c1c66aad642c44ccd85c887348baa44a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "3fbfe202d245b8eb6c2a398eeb827674c1c66aad642c44ccd85c887348baa44a", kill_on_drop: false }`
[INFO] [stdout] 3fbfe202d245b8eb6c2a398eeb827674c1c66aad642c44ccd85c887348baa44a
