granges 0.2.2

A Rust library and command line tool for genomic range operations.
Documentation
Build #1157409 2024-03-14 02:16:32

# rustc version rustc 1.78.0-nightly (3cbb93223 2024-03-13)

# docs.rs version docsrs 0.6.0 (e00048fe 2024-03-13)

# build log [INFO] running `Command { std: "docker" "create" "-v" "/home/cratesfyi/workspace-builder/builds/granges-0.2.2/target:/opt/rustwide/target:rw,Z" "-v" "/home/cratesfyi/workspace-builder/builds/granges-0.2.2/source:/opt/rustwide/workdir:ro,Z" "-v" "/home/cratesfyi/workspace-builder/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/home/cratesfyi/workspace-builder/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "DOCS_RS=1" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "6442450944" "--cpus" "6" "--user" "1001:1001" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+nightly" "rustdoc" "--lib" "-Zrustdoc-map" "--config" "build.rustdocflags=[\"--cfg\", \"docsrs\", \"-Z\", \"unstable-options\", \"--emit=invocation-specific\", \"--resource-suffix\", \"-20240313-1.78.0-nightly-3cbb93223\", \"--static-root-path\", \"/-/rustdoc.static/\", \"--cap-lints\", \"warn\", \"--extern-html-root-takes-precedence\"]" "--offline" "-Zunstable-options" "--config=doc.extern-map.registries.crates-io=\"https://docs.rs/{pkg_name}/{version}/x86_64-unknown-linux-gnu\"" "-Zrustdoc-scrape-examples" "-j6" "--target" "x86_64-unknown-linux-gnu", kill_on_drop: false }` [INFO] [stdout] ac594094d166911f350f01721bf96f36b2ea9deda257d1ccc6e79369661868cc [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "ac594094d166911f350f01721bf96f36b2ea9deda257d1ccc6e79369661868cc", kill_on_drop: false }` [INFO] [stderr] warning: Rustdoc did not scrape the following examples because they require dev-dependencies: mean_score [INFO] [stderr] If you want Rustdoc to scrape these examples, then add `doc-scrape-examples = true` [INFO] [stderr] to the [[example]] target configuration of at least one example. [INFO] [stderr] warning: target filter specified, but no targets matched; this is a no-op [INFO] [stderr] Documenting granges v0.2.2 (/opt/rustwide/workdir) [INFO] [stderr] warning: unresolved link to `GenomicRangeEmptyRecord` [INFO] [stderr] --> src/io/parsers/mod.rs:20:11 [INFO] [stderr] | [INFO] [stderr] 20 | //! 1. [`GenomicRangeEmptyRecord`], when a BED3 is loaded. This type indicates the incoming ranges [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ no item named `GenomicRangeEmptyRecord` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] = note: `#[warn(rustdoc::broken_intra_doc_links)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `GenomicRangeRecord` [INFO] [stderr] --> src/io/parsers/mod.rs:23:11 [INFO] [stderr] | [INFO] [stderr] 23 | //! 2. [`GenomicRangeRecord<Option<String>>`], which is a range record *possibly* (hence, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ no item named `GenomicRangeRecord` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `GenomicRangeRecord` [INFO] [stderr] --> src/io/parsers/mod.rs:27:11 [INFO] [stderr] | [INFO] [stderr] 27 | //! 3. [`GenomicRangeRecord<U>`], which is a range record with an *addition* set of data. [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ no item named `GenomicRangeRecord` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `GenomicRangeRecord` [INFO] [stderr] --> src/io/parsers/mod.rs:30:11 [INFO] [stderr] | [INFO] [stderr] 30 | //! [`GenomicRangeRecord<Bed5Addition>`] types. [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ no item named `GenomicRangeRecord` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `GenomicRangeRecord` [INFO] [stderr] --> src/io/parsers/bed/mod.rs:11:46 [INFO] [stderr] | [INFO] [stderr] 11 | //! returned by these parsing iterators is [`GenomicRangeRecord<U>`] where [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ no item named `GenomicRangeRecord` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `GenomicRangeRecordEmpty` [INFO] [stderr] --> src/io/parsers/bed/bed4.rs:1:48 [INFO] [stderr] | [INFO] [stderr] 1 | //! BED4 Parsers, which are built off of the [`GenomicRangeRecordEmpty`] [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ no item named `GenomicRangeRecordEmpty` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `Bed5Addition` [INFO] [stderr] --> src/io/parsers/bed/bed4.rs:22:21 [INFO] [stderr] | [INFO] [stderr] 22 | /// Note that the [`Bed5Addition`] is *permissive* in the sense [INFO] [stderr] | ^^^^^^^^^^^^ no item named `Bed5Addition` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `GenomicRangeRecordEmpty` [INFO] [stderr] --> src/io/parsers/bed/bed5.rs:1:48 [INFO] [stderr] | [INFO] [stderr] 1 | //! BED5 Parsers, which are built off of the [`GenomicRangeRecordEmpty`] [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ no item named `GenomicRangeRecordEmpty` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `parse_bedlike` [INFO] [stderr] --> src/io/parsers/bed/bedlike.rs:78:14 [INFO] [stderr] | [INFO] [stderr] 78 | /// Unlike [`parse_bedlike()`], this function returns a concrete [INFO] [stderr] | ^^^^^^^^^^^^^^^ no item named `parse_bedlike` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `Position` [INFO] [stderr] --> src/io/parsers/detect.rs:81:20 [INFO] [stderr] | [INFO] [stderr] 81 | /// into [`Position`] types, to check if this is a BED-like file (i.e. [INFO] [stderr] | ^^^^^^^^ no item named `Position` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `GenomicRangeRecord` [INFO] [stderr] --> src/io/parsers/tsv.rs:69:29 [INFO] [stderr] | [INFO] [stderr] 69 | /// convert a line into a [`GenomicRangeRecord<U>`], a range with generic associated [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^ no item named `GenomicRangeRecord` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `DatumType::NoValue` [INFO] [stderr] --> src/io/tsv.rs:16:21 [INFO] [stderr] | [INFO] [stderr] 16 | /// for `None` or [`DatumType::NoValue`]. [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^ no item named `DatumType` in scope [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `Result<GenomicRangeRecord<U>, GRangesError` [INFO] [stderr] --> src/merging_iterators.rs:356:32 [INFO] [stderr] | [INFO] [stderr] 356 | /// A merging iterator (over [`Result<GenomicRangeRecord<U>, GRangesError`] items, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ unbalanced angle brackets [INFO] [stderr] [INFO] [stderr] warning: unresolved link to `GenomicRangeEmptyRecord` [INFO] [stderr] --> src/io/parsers/filters.rs:103:51 [INFO] [stderr] | [INFO] [stderr] 103 | /// Range-filtering iterator implementation for [`GenomicRangeEmptyRecord`]. [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^ no item named `GenomicRangeEmptyRecord` in scope [INFO] [stderr] | [INFO] [stderr] = help: to escape `[` and `]` characters, add '\' before them like `\[` or `\]` [INFO] [stderr] [INFO] [stderr] warning: this URL is not a hyperlink [INFO] [stderr] --> src/commands.rs:747:19 [INFO] [stderr] | [INFO] [stderr] 747 | /// The xsv tool (https://github.com/BurntSushi/xsv) is useful for visualizing [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/BurntSushi/xsv>` [INFO] [stderr] | [INFO] [stderr] = note: bare URLs are not automatically turned into clickable links [INFO] [stderr] = note: `#[warn(rustdoc::bare_urls)]` on by default [INFO] [stderr] [INFO] [stderr] warning: `granges` (lib doc) generated 15 warnings (run `cargo fix --lib -p granges` to apply 1 suggestion) [INFO] [stderr] Finished `dev` profile [optimized + debuginfo] target(s) in 0.81s [INFO] [stderr] Generated /opt/rustwide/target/x86_64-unknown-linux-gnu/doc/granges/index.html [INFO] running `Command { std: "docker" "inspect" "ac594094d166911f350f01721bf96f36b2ea9deda257d1ccc6e79369661868cc", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ac594094d166911f350f01721bf96f36b2ea9deda257d1ccc6e79369661868cc", kill_on_drop: false }` [INFO] [stdout] ac594094d166911f350f01721bf96f36b2ea9deda257d1ccc6e79369661868cc