[INFO] cloning repository https://github.com/COMBINE-lab/piscem
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/COMBINE-lab/piscem" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fpiscem", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fpiscem'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] c202015892f57ec9c3bad13b521b81b7162e4e1c
[INFO] documenting COMBINE-lab/piscem against 1.99.0-beta.1 for beta-rustdoc-1.99-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fpiscem" "/workspace/builds/worker-2-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc2/source'...
[INFO] [stderr] done.
[INFO] removed /workspace/builds/worker-2-tc2/source/.cargo/config.toml
[INFO] started tweaking git repo https://github.com/COMBINE-lab/piscem
[INFO] finished tweaking git repo https://github.com/COMBINE-lab/piscem
[INFO] tweaked toml for git repo https://github.com/COMBINE-lab/piscem written to /workspace/builds/worker-2-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/COMBINE-lab/piscem on toolchain 1.99.0-beta.1
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.99.0-beta.1" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/COMBINE-lab/piscem 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" "+1.99.0-beta.1" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:00c5645b54fe3ce5dae1417175e3c7fb6a6646c021d554ecd63a097b8b9f3602" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 6473b9a3af63fee8a335715a1c8a7b58dc05bf27b1428e2733f3f89a31489cc3
[INFO] running `Command { std: "docker" "start" "6473b9a3af63fee8a335715a1c8a7b58dc05bf27b1428e2733f3f89a31489cc3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "6473b9a3af63fee8a335715a1c8a7b58dc05bf27b1428e2733f3f89a31489cc3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "6473b9a3af63fee8a335715a1c8a7b58dc05bf27b1428e2733f3f89a31489cc3" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.1" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "6473b9a3af63fee8a335715a1c8a7b58dc05bf27b1428e2733f3f89a31489cc3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "6473b9a3af63fee8a335715a1c8a7b58dc05bf27b1428e2733f3f89a31489cc3" "/opt/rustwide/cargo-home/bin/cargo" "+1.99.0-beta.1" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stderr]    Compiling proc-macro2 v1.0.107
[INFO] [stderr]    Compiling libc v0.2.189
[INFO] [stderr]    Compiling find-msvc-tools v0.1.10
[INFO] [stderr]    Compiling pkg-config v0.3.33
[INFO] [stderr]     Checking bitflags v2.13.1
[INFO] [stderr]     Checking allocator-api2 v0.2.21
[INFO] [stderr]    Compiling serde_core v1.0.229
[INFO] [stderr]     Checking aho-corasick v1.1.5
[INFO] [stderr]     Checking zlib-rs v0.6.7
[INFO] [stderr]    Compiling cfg_aliases v0.2.2
[INFO] [stderr]     Checking foldhash v0.2.0
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]    Compiling zstd-safe v7.2.4
[INFO] [stderr]     Checking simd-adler32 v0.3.10
[INFO] [stderr]    Compiling getrandom v0.4.3
[INFO] [stderr]    Compiling nix v0.30.1
[INFO] [stderr]     Checking bytes v1.12.1
[INFO] [stderr]     Checking byteorder v1.5.0
[INFO] [stderr]     Checking miniz_oxide v0.8.9
[INFO] [stderr]    Compiling object v0.39.1
[INFO] [stderr]    Compiling memchr v2.8.3
[INFO] [stderr]     Checking arrayvec v0.7.8
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]     Checking smallvec v1.15.2
[INFO] [stderr]     Checking hashbrown v0.16.1
[INFO] [stderr]    Compiling serde v1.0.229
[INFO] [stderr]    Compiling zerocopy v0.8.56
[INFO] [stderr]     Checking wyhash v0.5.0
[INFO] [stderr]     Checking crossbeam-channel v0.5.16
[INFO] [stderr]     Checking buffer-redux v1.1.0
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking bytecount v0.6.9
[INFO] [stderr]    Compiling prettyplease v0.2.37
[INFO] [stderr]     Checking jiff-core v0.1.0
[INFO] [stderr]     Checking rapidhash v1.4.0
[INFO] [stderr]     Checking dyn_size_of v0.4.5
[INFO] [stderr]     Checking combine v4.6.7
[INFO] [stderr]     Checking bitm v0.5.2
[INFO] [stderr]     Checking regex-automata v0.4.18
[INFO] [stderr]     Checking seedable_hash v0.2.3
[INFO] [stderr]     Checking hashbrown v0.17.1
[INFO] [stderr]    Compiling quote v1.0.47
[INFO] [stderr]     Checking flate2 v1.1.9
[INFO] [stderr]     Checking voracious_radix_sort v1.2.0
[INFO] [stderr]    Compiling syn v2.0.119
[INFO] [stderr]    Compiling syn v3.0.3
[INFO] [stderr]    Compiling proc-macro-error-attr2 v2.0.0
[INFO] [stderr]    Compiling jobserver v0.1.35
[INFO] [stderr]    Compiling either v1.17.0
[INFO] [stderr]     Checking libbz2-rs-sys v0.2.5
[INFO] [stderr]     Checking binout v0.3.1
[INFO] [stderr]     Checking xxhash-rust v0.8.18
[INFO] [stderr]    Compiling cc v1.4.2
[INFO] [stderr]    Compiling proc-macro-error2 v2.0.1
[INFO] [stderr]     Checking indexmap v2.14.0
[INFO] [stderr]    Compiling itertools v0.10.5
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking jiff v0.2.35
[INFO] [stderr]     Checking rand v0.10.2
[INFO] [stderr]     Checking bzip2 v0.6.1
[INFO] [stderr]     Checking sysinfo v0.36.1
[INFO] [stderr]     Checking num-format v0.4.4
[INFO] [stderr]     Checking fallible-iterator v0.3.0
[INFO] [stderr]     Checking aliasable v0.1.3
[INFO] [stderr]     Checking stable_try_trait_v2 v1.75.1
[INFO] [stderr]     Checking fastrand v2.5.0
[INFO] [stderr]     Checking maybe-dangling v0.1.2
[INFO] [stderr]     Checking arbitrary-chunks v0.4.1
[INFO] [stderr]     Checking partition v0.1.2
[INFO] [stderr]     Checking lambert_w v1.2.34
[INFO] [stderr]     Checking parking_lot_core v0.9.12
[INFO] [stderr]     Checking rdst v0.20.14
[INFO] [stderr]     Checking thread-priority v3.1.1
[INFO] [stderr]    Compiling ahash v0.8.12
[INFO] [stderr]     Checking num-primitive v0.2.1
[INFO] [stderr]     Checking foldhash v0.1.5
[INFO] [stderr]     Checking terminal_size v0.4.4
[INFO] [stderr]     Checking tempfile v3.27.0
[INFO] [stderr]     Checking sync-cell-slice v0.9.14
[INFO] [stderr]     Checking ensure_simd v0.1.0
[INFO] [stderr]     Checking clap_builder v4.6.6
[INFO] [stderr]    Compiling toml_write v0.1.2
[INFO] [stderr]     Checking atomic-primitive v0.1.4
[INFO] [stderr]     Checking hashbrown v0.15.5
[INFO] [stderr]     Checking sharded-slab v0.1.7
[INFO] [stderr]     Checking getrandom v0.3.4
[INFO] [stderr]     Checking ph-temp v0.12.0
[INFO] [stderr]     Checking memmap2 v0.9.11
[INFO] [stderr]    Compiling zstd-sys v2.0.16+zstd.1.5.7
[INFO] [stderr]    Compiling liblzma-sys v0.3.13
[INFO] [stderr]     Checking regex v1.13.1
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling stacker v0.1.25
[INFO] [stderr]    Compiling serde_spanned v0.6.9
[INFO] [stderr]    Compiling toml_datetime v0.6.11
[INFO] [stderr]    Compiling sha2-asm v0.6.4
[INFO] [stderr]    Compiling toml_edit v0.22.27
[INFO] [stderr]     Checking env_filter v2.0.0
[INFO] [stderr]     Checking pluralizer v0.5.0
[INFO] [stderr]     Checking bzip2 v0.5.2
[INFO] [stderr]     Checking dsi-progress-logger v0.8.9
[INFO] [stderr]     Checking liblzma v0.3.6
[INFO] [stderr]     Checking serde_json v1.0.151
[INFO] [stderr]     Checking matchers v0.2.0
[INFO] [stderr]    Compiling libmimalloc-sys v0.1.49
[INFO] [stderr]     Checking tracing-log v0.2.0
[INFO] [stderr]     Checking rapidhash v4.5.1
[INFO] [stderr]     Checking thread_local v1.1.10
[INFO] [stderr]     Checking nu-ansi-term v0.50.3
[INFO] [stderr]     Checking yansi v1.0.1
[INFO] [stderr]    Compiling seq-macro v0.3.6
[INFO] [stderr]     Checking unicode-width v0.1.14
[INFO] [stderr]     Checking unicode-ident v1.0.24
[INFO] [stderr]     Checking console v0.16.4
[INFO] [stderr]     Checking ariadne v0.5.1
[INFO] [stderr]     Checking digest v0.10.7
[INFO] [stderr]     Checking bzip2 v0.4.4
[INFO] [stderr]     Checking parking_lot v0.12.5
[INFO] [stderr]     Checking cpu-time v1.0.0
[INFO] [stderr]     Checking num_cpus v1.17.0
[INFO] [stderr]     Checking libz-rs-sys v0.6.7
[INFO] [stderr]     Checking crossbeam-queue v0.3.13
[INFO] [stderr]     Checking itertools v0.15.0
[INFO] [stderr]     Checking hashbrown v0.14.5
[INFO] [stderr]     Checking sha2 v0.10.9
[INFO] [stderr]     Checking crossbeam v0.8.4
[INFO] [stderr]     Checking ph v0.11.0
[INFO] [stderr]     Checking path-tools v0.1.0
[INFO] [stderr]     Checking nohash-hasher v0.2.0
[INFO] [stderr]     Checking indicatif v0.18.6
[INFO] [stderr]    Compiling ar_archive_writer v0.5.3
[INFO] [stderr]    Compiling derivative v2.2.0
[INFO] [stderr]    Compiling darling_core v0.21.3
[INFO] [stderr]    Compiling darling_core v0.23.0
[INFO] [stderr]    Compiling impl-tools-lib v0.11.4
[INFO] [stderr]     Checking env_logger v0.11.11
[INFO] [stderr]     Checking dashmap v6.2.1
[INFO] [stderr]    Compiling thiserror-impl v2.0.20
[INFO] [stderr]    Compiling bytemuck_derive v1.12.0
[INFO] [stderr]    Compiling clap_derive v4.6.4
[INFO] [stderr]    Compiling serde_derive v1.0.229
[INFO] [stderr]     Checking mimalloc v0.1.52
[INFO] [stderr]    Compiling psm v0.1.32
[INFO] [stderr]    Compiling toml v0.8.23
[INFO] [stderr]     Checking thiserror v2.0.20
[INFO] [stderr]     Checking chumsky v0.12.0
[INFO] [stderr]    Compiling piscem v0.22.1 (/opt/rustwide/workdir)
[INFO] [stderr]     Checking bytemuck v1.25.2
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling enum-as-inner v0.6.1
[INFO] [stderr]    Compiling mem_dbg-derive v0.3.4
[INFO] [stderr]    Compiling zerocopy-derive v0.8.56
[INFO] [stderr]    Compiling tracing-attributes v0.1.31
[INFO] [stderr]     Checking safe_arch v1.1.0
[INFO] [stderr]    Compiling value-traits-derive v0.2.1
[INFO] [stderr]    Compiling epserde-derive v0.12.5
[INFO] [stderr]    Compiling sealed v0.6.0
[INFO] [stderr]    Compiling lender-derive v0.1.3
[INFO] [stderr]     Checking wide v1.6.1
[INFO] [stderr]     Checking clap v4.6.6
[INFO] [stderr]     Checking succinctly v0.6.0
[INFO] [stderr]     Checking lender v0.6.2
[INFO] [stderr]    Compiling impl-tools v0.11.4
[INFO] [stderr]     Checking value-traits v0.2.1
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]    Compiling ambassador v0.5.1
[INFO] [stderr]     Checking sysctl v0.6.0
[INFO] [stderr]    Compiling darling_macro v0.23.0
[INFO] [stderr]     Checking mmap-rs v0.7.0
[INFO] [stderr]     Checking tracing v0.1.44
[INFO] [stderr]     Checking bgzip v0.3.1
[INFO] [stderr]    Compiling darling v0.23.0
[INFO] [stderr]    Compiling bon-macros v3.9.3
[INFO] [stderr]     Checking mem_dbg v0.4.4
[INFO] [stderr]     Checking tracing-subscriber v0.3.23
[INFO] [stderr]    Compiling darling_macro v0.21.3
[INFO] [stderr]     Checking epserde v0.12.6
[INFO] [stderr]    Compiling darling v0.21.3
[INFO] [stderr]    Compiling derive_setters v0.1.9
[INFO] [stderr]     Checking seq_geom_parser v1.1.0
[INFO] [stderr]     Checking thread-broker v0.1.0
[INFO] [stderr]     Checking zstd v0.13.3
[INFO] [stderr]     Checking needletail v0.7.3
[INFO] [stderr]     Checking niffler v3.0.0
[INFO] [stderr]     Checking needletail v0.6.3
[INFO] [stderr]     Checking paraseq-temp v0.5.0-pre.2
[INFO] [stderr]     Checking prepare_fasta v0.2.0
[INFO] [stderr]     Checking bon v3.9.3
[INFO] [stderr]     Checking rapidgzip-core v0.3.1
[INFO] [stderr]     Checking packed-seq v5.0.0
[INFO] [stderr]     Checking sux v0.14.0
[INFO] [stderr]     Checking seq-hash v0.2.0
[INFO] [stderr]     Checking simd-minimizers v3.0.0
[INFO] [stderr]     Checking cf1-rs v0.5.1
[INFO] [stderr]     Checking sshash-lib v0.6.4
[INFO] [stderr]     Checking tiny-dict v0.6.4
[INFO] [stderr]     Checking piscem-rs v0.9.2
[INFO] [stderr]  Documenting piscem v0.22.1 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unresolved link to `DEPRECATED`
[INFO] [stdout]    --> src/piscem_commands.rs:432:10
[INFO] [stdout]     |
[INFO] [stdout] 432 |     /// [DEPRECATED] apply structural constraints when performing mapping.
[INFO] [stdout]     |          ^^^^^^^^^^ no item named `DEPRECATED` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout]     = note: `#[warn(rustdoc::broken_intra_doc_links)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `DEPRECATED`
[INFO] [stdout]    --> src/piscem_commands.rs:441:10
[INFO] [stdout]     |
[INFO] [stdout] 441 |     /// [DEPRECATED] output mappings in sam format.
[INFO] [stdout]     |          ^^^^^^^^^^ no item named `DEPRECATED` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `DEPRECATED`
[INFO] [stdout]    --> src/piscem_commands.rs:446:10
[INFO] [stdout]     |
[INFO] [stdout] 446 |     /// [DEPRECATED] output mappings in bed format.
[INFO] [stdout]     |          ^^^^^^^^^^ no item named `DEPRECATED` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `DEPRECATED`
[INFO] [stdout]    --> src/piscem_commands.rs:451:10
[INFO] [stdout]     |
[INFO] [stdout] 451 |     /// [DEPRECATED] use chromosomes as color.
[INFO] [stdout]     |          ^^^^^^^^^^ no item named `DEPRECATED` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unresolved link to `DEPRECATED`
[INFO] [stdout]    --> src/piscem_commands.rs:472:10
[INFO] [stdout]     |
[INFO] [stdout] 472 |     /// [DEPRECATED] Check if any mapping kmer exist for a mate which is not mapped,
[INFO] [stdout]     |          ^^^^^^^^^^ no item named `DEPRECATED` in scope
[INFO] [stdout]     |
[INFO] [stdout]     = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 20s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: proc-macro-error2 v2.0.1
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 6`
[INFO] [stderr]    Generated /opt/rustwide/target/doc/piscem/index.html
[INFO] running `Command { std: "docker" "inspect" "6473b9a3af63fee8a335715a1c8a7b58dc05bf27b1428e2733f3f89a31489cc3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "6473b9a3af63fee8a335715a1c8a7b58dc05bf27b1428e2733f3f89a31489cc3", kill_on_drop: false }`
[INFO] [stdout] 6473b9a3af63fee8a335715a1c8a7b58dc05bf27b1428e2733f3f89a31489cc3
