[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 }`
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[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 }`
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[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