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The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected]. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

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The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

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warning: dereferencing a tuple pattern where every element takes a reference --> src/strand.rs:296:36 | 296 | (&Option::Some(ref x), &Option::Some(ref x1)) => x.same(x1), | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrowed_reference help: try removing the `&` and `ref` parts | 296 - (&Option::Some(ref x), &Option::Some(ref x1)) => x.same(x1), 296 + (&Option::Some(ref x), Option::Some(x1)) => x.same(x1), |

warning: dereferencing a tuple pattern where every element takes a reference --> src/strand.rs:296:14 | 296 | (&Option::Some(ref x), &Option::Some(ref x1)) => x.same(x1), | ^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrowed_reference = note: `#[warn(clippy::needless_borrowed_reference)]` on by default help: try removing the `&` and `ref` parts | 296 - (&Option::Some(ref x), &Option::Some(ref x1)) => x.same(x1), 296 + (Option::Some(x), &Option::Some(ref x1)) => x.same(x1), |

warning: this `impl` can be derived --> src/sequence.rs:61:1 | 61 | / impl Default for SequenceReadPairOrientation { 62 | | fn default() -> Self { 63 | | None 64 | | } 65 | | } | |_^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#derivable_impls = help: remove the manual implementation... help: ...and instead derive it... | 49 + #[derive(Default)] 50 | pub enum SequenceReadPairOrientation { | help: ...and mark the default variant | 58 ~ #[default] 59 ~ None, |

warning: non-canonical implementation of `partial_cmp` on an `Ord` type --> src/genome.rs:32:1 | 32 | / impl PartialOrd for Interval { 33 | | fn partial_cmp(&self, other: &Self) -> Option<cmp::Ordering> { | | __________________________________________________________________- 34 | || Some(self.contig.cmp(&other.contig).then_with(|| { 35 | || self.range 36 | || .start ... || 39 | || })) 40 | || } | ||_____- help: change this to: `{ Some(std::cmp::Ord::cmp(self, other)) }` 41 | | } | |__^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#non_canonical_partial_ord_impl = note: `#[warn(clippy::non_canonical_partial_ord_impl)]` on by default

warning: this pattern creates a reference to a reference --> src/annot/refids.rs:70:25 | 70 | if let Some(ref r) = self.refids.get(id) { | ^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow = note: `#[warn(clippy::needless_borrow)]` on by default help: try | 70 ~ if let Some(r) = self.refids.get(id) { 71 ~ r.clone() |

warning: doc list item missing indentation --> src/annot/pos.rs:125:9 | 125 | /// features. | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 125 | /// features. | ++

warning: doc list item missing indentation --> src/annot/pos.rs:124:9 | 124 | /// forward-strand features and increase it for reverse-strand | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 124 | /// forward-strand features and increase it for reverse-strand | ++

warning: doc list item missing indentation --> src/annot/pos.rs:123:9 | 123 | /// positive `dist` will numerically decrease the position for | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 123 | /// positive `dist` will numerically decrease the position for | ++

warning: doc list item missing indentation --> src/annot/pos.rs:94:9 | 94 | /// features. | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 94 | /// features. | ++

warning: doc list item missing indentation --> src/annot/pos.rs:93:9 | 93 | /// forward-strand features and decrease it for reverse-strand | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 93 | /// forward-strand features and decrease it for reverse-strand | ++

warning: doc list item missing indentation --> src/annot/pos.rs:92:9 | 92 | /// positive `dist` will numerically increase the position for | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 92 | /// positive `dist` will numerically increase the position for | ++

warning: doc list item missing indentation --> src/annot/contig.rs:175:9 | 175 | /// expand for reverse-strand annotations. | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 175 | /// expand for reverse-strand annotations. | ++

warning: doc list item missing indentation --> src/annot/contig.rs:174:9 | 174 | /// forward-strand annotations and the left, 5'-most end will | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 174 | /// forward-strand annotations and the left, 5'-most end will | ++

warning: doc list item missing indentation --> src/annot/contig.rs:173:9 | 173 | /// right, 3'-most end of the contig will expand for | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 173 | /// right, 3'-most end of the contig will expand for | ++

warning: doc list item missing indentation --> src/annot/contig.rs:148:9 | 148 | /// reverse-strand annotations. | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 148 | /// reverse-strand annotations. | ++

warning: doc list item missing indentation --> src/annot/contig.rs:147:9 | 147 | /// annotations and the right, 3'-most end will expand for | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation help: indent this line | 147 | /// annotations and the right, 3'-most end will expand for | ++

warning: doc list item missing indentation --> src/annot/contig.rs:146:9 | 146 | /// left, 5'-most end of the contig will expand for forward-strand | ^ | = help: if this is supposed to be its own paragraph, add a blank line = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#doc_lazy_continuation = note: `#[warn(clippy::doc_lazy_continuation)]` on by default help: indent this line | 146 | /// left, 5'-most end of the contig will expand for forward-strand | ++

warning: this `impl` can be derived --> src/alignment.rs:52:1 | 52 | / impl Default for AlignmentMode { 53 | | fn default() -> Self { 54 | | AlignmentMode::Global 55 | | } 56 | | } | |_^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#derivable_impls = note: `#[warn(clippy::derivable_impls)]` on by default = help: remove the manual implementation... help: ...and instead derive it... | 45 + #[derive(Default)] 46 | pub enum AlignmentMode { | help: ...and mark the default variant | 48 ~ #[default] 49 ~ Global, |

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/clippy-check@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/clippy-check@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

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The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/cargo@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/cargo@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

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only one of `license` or `license-file` is necessary

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The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/cargo@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/cargo@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

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only one of `license` or `license-file` is necessary

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The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/cargo@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/cargo@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

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The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

only one of `license` or `license-file` is necessary

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The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/[email protected]. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected], actions-rs/[email protected], coverallsapp/github-action@master. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

Unable to download cargo-tarpaulin == latest from the tool cache: Error: Unexpected HTTP response: 403

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The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/