[INFO] cloning repository https://github.com/COMBINE-lab/simpleaf
[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/simpleaf" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fsimpleaf", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fsimpleaf'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 7203ce392bc8c52f6cfc212b96d8b41b18755183
[INFO] documenting COMBINE-lab/simpleaf against 1.85.0 for beta-1.86-rustdoc-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fsimpleaf" "/workspace/builds/worker-7-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-7-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/COMBINE-lab/simpleaf on toolchain 1.85.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.85.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] started tweaking git repo https://github.com/COMBINE-lab/simpleaf
[INFO] finished tweaking git repo https://github.com/COMBINE-lab/simpleaf
[INFO] tweaked toml for git repo https://github.com/COMBINE-lab/simpleaf written to /workspace/builds/worker-7-tc1/source/Cargo.toml
[INFO] crate git repo https://github.com/COMBINE-lab/simpleaf 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" "+1.85.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/af-anndata`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/roers`
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/seq_geom_parser`
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/seq_geom_xform`
[INFO] [stderr]     Updating git repository `https://github.com/COMBINE-lab/grangers.git`
[INFO] [stderr]  Downloading crates ...
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/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@sha256:3959728d45483eb673ba100a951a6b9f5012970368db2a9e08e0ac9b67c8a5ad" "/opt/rustwide/cargo-home/bin/cargo" "+1.85.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 9ac42b231b1616d81da3d5ac68938ed6cce6ae816ada39ada61d825802ba16c0
[INFO] running `Command { std: "docker" "start" "-a" "9ac42b231b1616d81da3d5ac68938ed6cce6ae816ada39ada61d825802ba16c0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "9ac42b231b1616d81da3d5ac68938ed6cce6ae816ada39ada61d825802ba16c0", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "9ac42b231b1616d81da3d5ac68938ed6cce6ae816ada39ada61d825802ba16c0", kill_on_drop: false }`
[INFO] [stdout] 9ac42b231b1616d81da3d5ac68938ed6cce6ae816ada39ada61d825802ba16c0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-7-tc1/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@sha256:3959728d45483eb673ba100a951a6b9f5012970368db2a9e08e0ac9b67c8a5ad" "/opt/rustwide/cargo-home/bin/cargo" "+1.85.0" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 5837bb6aba472233356953c42281ebf283a992e0730487487a88e67e16fb442f
[INFO] running `Command { std: "docker" "start" "-a" "5837bb6aba472233356953c42281ebf283a992e0730487487a88e67e16fb442f", kill_on_drop: false }`
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[INFO] [stderr]  Documenting simpleaf v0.19.2 (/opt/rustwide/workdir)
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]   --> src/utils/prog_utils.rs:46:56
[INFO] [stdout]    |
[INFO] [stdout] 46 | /// this is a limitation put in place by `ureq` (see : https://docs.rs/ureq/3.0.0-rc4/ureq/struct.Body.html#method.read_json)
[INFO] [stdout]    |                                                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout]    = note: `#[warn(rustdoc::bare_urls)]` on by default
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]    |
[INFO] [stdout] 46 | /// this is a limitation put in place by `ureq` (see : <https://docs.rs/ureq/3.0.0-rc4/ureq/struct.Body.html#method.read_json>)
[INFO] [stdout]    |                                                        +                                                                     +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]     --> src/utils/workflow_utils.rs:1341:18
[INFO] [stdout]      |
[INFO] [stdout] 1341 | /// Adapted from https://stackoverflow.com/a/65192210.
[INFO] [stdout]      |                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]      |
[INFO] [stdout] 1341 | /// Adapted from <https://stackoverflow.com/a/65192210.>
[INFO] [stdout]      |                  +                                     +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: this URL is not a hyperlink
[INFO] [stdout]    --> src/simpleaf_commands/workflow.rs:187:43
[INFO] [stdout]     |
[INFO] [stdout] 187 | /// from the protocol estuary GitHub repo https://github.com/COMBINE-lab/protocol-estuary
[INFO] [stdout]     |                                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: bare URLs are not automatically turned into clickable links
[INFO] [stdout] help: use an automatic link instead
[INFO] [stdout]     |
[INFO] [stdout] 187 | /// from the protocol estuary GitHub repo <https://github.com/COMBINE-lab/protocol-estuary>
[INFO] [stdout]     |                                           +                                               +
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 25s
[INFO] [stderr]    Generated /opt/rustwide/target/doc/simpleaf/index.html
[INFO] running `Command { std: "docker" "inspect" "5837bb6aba472233356953c42281ebf283a992e0730487487a88e67e16fb442f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "5837bb6aba472233356953c42281ebf283a992e0730487487a88e67e16fb442f", kill_on_drop: false }`
[INFO] [stdout] 5837bb6aba472233356953c42281ebf283a992e0730487487a88e67e16fb442f
