error[E0432]: unresolved import `crate::vdj_types` --> vdj_ann/src/transcript.rs:7:12 | 7 | use crate::vdj_types::{VdjChain, VDJ_CHAINS}; | ^^^^^^^^^ could not find `vdj_types` in the crate root

error: unused import: `io_utils::fwriteln` --> vdj_ann/src/transcript.rs:11:5 | 11 | use io_utils::fwriteln; | ^^^^^^^^^^^^^^^^^^ | = note: `-D unused-imports` implied by `-D unused`

error: unused import: `std::str::FromStr` --> vdj_ann/src/transcript.rs:14:5 | 14 | use std::str::FromStr; | ^^^^^^^^^^^^^^^^^

error: unused import: `io::prelude::*` --> vdj_ann/src/transcript.rs:15:21 | 15 | use std::{cmp::max, io::prelude::*}; | ^^^^^^^^^^^^^^

error[E0277]: the trait bound `transcript::ContigStatus: annotate::_::_serde::Serialize` is not satisfied --> vdj_ann/src/annotate.rs:2972:17 | 2972 | #[derive(Debug, Serialize, Deserialize, Clone, PartialEq)] | ^^^^^^^^^ the trait `annotate::_::_serde::Serialize` is not implemented for `transcript::ContigStatus` ... 3021 | #[serde(skip_serializing_if = "Option::is_none")] | - required by a bound introduced by this call | = help: the following other types implement trait `annotate::_::_serde::Serialize`: &'a T &'a mut T () (T0, T1) (T0, T1, T2) (T0, T1, T2, T3) (T0, T1, T2, T3, T4) (T0, T1, T2, T3, T4, T5) and 154 others = note: required for `std::option::Option<transcript::ContigStatus>` to implement `annotate::_::_serde::Serialize` note: required by a bound in `annotate::_::_serde::ser::SerializeStruct::serialize_field` --> /home/runner/.cargo/registry/src/index.crates.io-6f17d22bba15001f/serde-1.0.188/src/ser/mod.rs:1865:12 | 1865 | T: Serialize; | ^^^^^^^^^ required by this bound in `SerializeStruct::serialize_field`

error[E0277]: the trait bound `transcript::ContigStatus: annotate::_::_serde::Deserialize<'_>` is not satisfied --> vdj_ann/src/annotate.rs:3022:30 | 3022 | pub productive_criteria: Option<ContigStatus>, | ^^^^^^^^^^^^^^^^^^^^ the trait `annotate::_::_serde::Deserialize<'_>` is not implemented for `transcript::ContigStatus` | = help: the following other types implement trait `annotate::_::_serde::Deserialize<'de>`: &'a [u8] &'a std::path::Path &'a str () (T0, T1) (T0, T1, T2) (T0, T1, T2, T3) (T0, T1, T2, T3, T4) and 160 others = note: required for `std::option::Option<transcript::ContigStatus>` to implement `annotate::_::_serde::Deserialize<'_>` note: required by a bound in `annotate::_::_serde::de::SeqAccess::next_element` --> /home/runner/.cargo/registry/src/index.crates.io-6f17d22bba15001f/serde-1.0.188/src/de/mod.rs:1724:12 | 1724 | T: Deserialize<'de>, | ^^^^^^^^^^^^^^^^ required by this bound in `SeqAccess::next_element`

error[E0277]: the trait bound `transcript::ContigStatus: annotate::_::_serde::Deserialize<'_>` is not satisfied --> vdj_ann/src/annotate.rs:3022:30 | 3022 | pub productive_criteria: Option<ContigStatus>, | ^^^^^^^^^^^^^^^^^^^^ the trait `annotate::_::_serde::Deserialize<'_>` is not implemented for `transcript::ContigStatus` | = help: the following other types implement trait `annotate::_::_serde::Deserialize<'de>`: &'a [u8] &'a std::path::Path &'a str () (T0, T1) (T0, T1, T2) (T0, T1, T2, T3) (T0, T1, T2, T3, T4) and 160 others = note: required for `std::option::Option<transcript::ContigStatus>` to implement `annotate::_::_serde::Deserialize<'_>` note: required by a bound in `annotate::_::_serde::de::MapAccess::next_value` --> /home/runner/.cargo/registry/src/index.crates.io-6f17d22bba15001f/serde-1.0.188/src/de/mod.rs:1863:12 | 1863 | V: Deserialize<'de>, | ^^^^^^^^^^^^^^^^ required by this bound in `MapAccess::next_value`

error[E0277]: the trait bound `transcript::ContigStatus: annotate::_::_serde::Deserialize<'_>` is not satisfied --> vdj_ann/src/annotate.rs:3021:5 | 3021 | #[serde(skip_serializing_if = "Option::is_none")] | ^ the trait `annotate::_::_serde::Deserialize<'_>` is not implemented for `transcript::ContigStatus` | = help: the following other types implement trait `annotate::_::_serde::Deserialize<'de>`: &'a [u8] &'a std::path::Path &'a str () (T0, T1) (T0, T1, T2) (T0, T1, T2, T3) (T0, T1, T2, T3, T4) and 160 others = note: required for `std::option::Option<transcript::ContigStatus>` to implement `annotate::_::_serde::Deserialize<'_>` note: required by a bound in `annotate::_::_serde::__private::de::missing_field` --> /home/runner/.cargo/registry/src/index.crates.io-6f17d22bba15001f/serde-1.0.188/src/private/de.rs:25:8 | 25 | V: Deserialize<'de>, | ^^^^^^^^^^^^^^^^ required by this bound in `missing_field`

error[E0369]: binary operation `==` cannot be applied to type `std::option::Option<transcript::ContigStatus>` --> vdj_ann/src/annotate.rs:3022:5 | 2972 | #[derive(Debug, Serialize, Deserialize, Clone, PartialEq)] | --------- in this derive macro expansion ... 3022 | pub productive_criteria: Option<ContigStatus>, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | note: an implementation of `std::cmp::PartialEq` might be missing for `transcript::ContigStatus` --> vdj_ann/src/transcript.rs:27:1 | 27 | pub struct ContigStatus { | ^^^^^^^^^^^^^^^^^^^^^^^ must implement `std::cmp::PartialEq` = note: this error originates in the derive macro `PartialEq` (in Nightly builds, run with -Z macro-backtrace for more info) help: consider annotating `transcript::ContigStatus` with `#[derive(PartialEq)]` --> |vdj_ann/src/transcript.rs:27:1 | 27 | #[derive(PartialEq)] |

Clippy had exited with the 101 exit code

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/cache@v3, 10XGenomics/clippy-check@main. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

warning: calling `set_len()` immediately after reserving a buffer creates uninitialized values --> vector_utils/src/lib.rs:490:5 | 490 | x.reserve(n); | ^^^^^^^^^^^^^ 491 | x.set_len(n); /* unsafe */ | ^^^^^^^^^^^^ | = help: initialize the buffer or wrap the content in `MaybeUninit` = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#uninit_vec note: the lint level is defined here --> vector_utils/src/lib.rs:487:8 | 487 | #[warn(clippy::uninit_vec)] | ^^^^^^^^^^^^^^^^^^