``` cargo clippy --fix Checking mehari v0.1.0 (/home/holtgrem_c/Development/mehari) warning: failed to automatically apply fixes suggested by rustc to crate `mehari` after fixes were automatically applied the compiler reported errors within these files: * /home/holtgrem_c/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/convert/mod.rs * /home/holtgrem_c/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/pin.rs * src/db/create/seqvar_freqs/reading.rs This likely indicates a bug in either rustc or cargo itself, and we would appreciate a bug report! You're likely to see a number of compiler warnings after this message which cargo attempted to fix but failed. If you could open an issue at https://github.com/rust-lang/rust/issues quoting the full output of this command we'd be very appreciative! Note that you may be able to make some more progress in the near-term fixing code with the `--broken-code` flag The following errors were reported: error[E0308]: mismatched types --> src/db/create/seqvar_freqs/reading.rs:86:13 | 86 | readers, | ^^^^^^^ expected struct `noodles_util::variant::Reader`, found struct `std::boxed::Box` | = note: expected struct `std::vec::Vec<noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` found struct `std::vec::Vec<std::boxed::Box<noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>>` error[E0308]: mismatched types --> src/db/create/seqvar_freqs/reading.rs:87:13 | 87 | headers, | ^^^^^^^ expected struct `noodles::noodles_vcf::Header`, found struct `std::boxed::Box` | = note: expected struct `std::vec::Vec<noodles::noodles_vcf::Header>` found struct `std::vec::Vec<std::boxed::Box<noodles::noodles_vcf::Header>>` error[E0599]: no method named `as_mut` found for struct `noodles_util::variant::Reader` in the current scope --> src/db/create/seqvar_freqs/reading.rs:114:14 | 114 | .as_mut() | ^^^^^^ method not found in `noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>` | ::: /home/holtgrem_c/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/convert/mod.rs:373:8 | 373 | fn as_mut(&mut self) -> &mut T; | ------ | | | the method is available for `std::boxed::Box<noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` here | the method is available for `std::boxed::Box<&mut noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` here | the method is available for `std::boxed::Box<&noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` here | ::: /home/holtgrem_c/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/pin.rs:701:12 | 701 | pub fn as_mut(&mut self) -> Pin<&mut P::Target> { | ------ the method is available for `std::pin::Pin<&mut noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` here | help: consider wrapping the receiver expression with the appropriate type | 113 | self.nexts[self.next] = Box::new(self.readers[self.next]) | +++++++++ + help: consider wrapping the receiver expression with the appropriate type | 113 | self.nexts[self.next] = Box::new(&mut self.readers[self.next]) | +++++++++++++ + help: consider wrapping the receiver expression with the appropriate type | 113 | self.nexts[self.next] = Pin::new(&mut self.readers[self.next]) | +++++++++++++ + help: consider wrapping the receiver expression with the appropriate type | 113 | self.nexts[self.next] = Box::new(&self.readers[self.next]) | ++++++++++ + error: aborting due to 3 previous errors Some errors have detailed explanations: E0308, E0599. For more information about an error, try `rustc --explain E0308`. Original diagnostics will follow. error[E0308]: mismatched types --> src/db/create/seqvar_freqs/reading.rs:86:13 | 86 | readers, | ^^^^^^^ expected struct `noodles_util::variant::Reader`, found struct `std::boxed::Box` | = note: expected struct `std::vec::Vec<noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` found struct `std::vec::Vec<std::boxed::Box<noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>>` error[E0308]: mismatched types --> src/db/create/seqvar_freqs/reading.rs:87:13 | 87 | headers, | ^^^^^^^ expected struct `noodles::noodles_vcf::Header`, found struct `std::boxed::Box` | = note: expected struct `std::vec::Vec<noodles::noodles_vcf::Header>` found struct `std::vec::Vec<std::boxed::Box<noodles::noodles_vcf::Header>>` error[E0599]: no method named `as_mut` found for struct `noodles_util::variant::Reader` in the current scope --> src/db/create/seqvar_freqs/reading.rs:114:14 | 114 | .as_mut() | ^^^^^^ method not found in `noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>` | ::: /home/holtgrem_c/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/convert/mod.rs:373:8 | 373 | fn as_mut(&mut self) -> &mut T; | ------ | | | the method is available for `std::boxed::Box<noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` here | the method is available for `std::boxed::Box<&mut noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` here | the method is available for `std::boxed::Box<&noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` here | ::: /home/holtgrem_c/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/pin.rs:701:12 | 701 | pub fn as_mut(&mut self) -> Pin<&mut P::Target> { | ------ the method is available for `std::pin::Pin<&mut noodles_util::variant::Reader<std::boxed::Box<(dyn std::io::BufRead + 'static)>>>` here | help: consider wrapping the receiver expression with the appropriate type | 113 | self.nexts[self.next] = Box::new(self.readers[self.next]) | +++++++++ + help: consider wrapping the receiver expression with the appropriate type | 113 | self.nexts[self.next] = Box::new(&mut self.readers[self.next]) | +++++++++++++ + help: consider wrapping the receiver expression with the appropriate type | 113 | self.nexts[self.next] = Pin::new(&mut self.readers[self.next]) | +++++++++++++ + help: consider wrapping the receiver expression with the appropriate type | 113 | self.nexts[self.next] = Box::new(&self.readers[self.next]) | ++++++++++ + Some errors have detailed explanations: E0308, E0599. For more information about an error, try `rustc --explain E0308`. error: could not compile `mehari` due to 3 previous errors warning: build failed, waiting for other jobs to finish... warning: use of `expect` followed by a function call --> src/db/create/seqvar_freqs/reading.rs:40:18 | 40 | .expect(&format!("Invalid contig {}", s)), | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try this: `unwrap_or_else(|| panic!("Invalid contig {}", s))` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#expect_fun_call = note: `#[warn(clippy::expect_fun_call)]` on by default warning: variables can be used directly in the `format!` string --> src/db/create/seqvar_freqs/reading.rs:40:26 | 40 | .expect(&format!("Invalid contig {}", s)), | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#uninlined_format_args = note: `#[warn(clippy::uninlined_format_args)]` on by default help: change this to | 40 - .expect(&format!("Invalid contig {}", s)), 40 + .expect(&format!("Invalid contig {s}")), | warning: `Vec<T>` is already on the heap, the boxing is unnecessary --> src/db/create/seqvar_freqs/reading.rs:50:14 | 50 | readers: Vec<Box<VariantReader<Box<dyn BufRead>>>>, | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `Vec<VariantReader<Box<dyn BufRead>>>` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#vec_box = note: `#[warn(clippy::vec_box)]` on by default warning: `Vec<T>` is already on the heap, the boxing is unnecessary --> src/db/create/seqvar_freqs/reading.rs:52:14 | 52 | headers: Vec<Box<VcfHeader>>, | ^^^^^^^^^^^^^^^^^^^ help: try: `Vec<VcfHeader>` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#vec_box warning: using `clone` on type `usize` which implements the `Copy` trait --> src/db/create/seqvar_freqs/reading.rs:179:28 | 179 | if lengths.get(idx).unwrap().clone() == length { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try dereferencing it: `*lengths.get(idx).unwrap()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#clone_on_copy = note: `#[warn(clippy::clone_on_copy)]` on by default warning: useless use of `vec!` --> src/db/create/seqvar_freqs/reading.rs:288:13 | 288 | / &vec![ 289 | | "tests/data/db/create/seqvar_freqs/gnomad.chrM.vcf", 290 | | "tests/data/db/create/seqvar_freqs/helix.chrM.vcf", 291 | | ], | |_____________^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_vec = note: `#[warn(clippy::useless_vec)]` on by default help: you can use a slice directly | 288 ~ &["tests/data/db/create/seqvar_freqs/gnomad.chrM.vcf", 289 ~ "tests/data/db/create/seqvar_freqs/helix.chrM.vcf"], | warning: an implementation of `From` is preferred since it gives you `Into<_>` for free where the reverse isn't true --> src/db/create/seqvar_freqs/serialized.rs:132:1 | 132 | impl Into<Vec<u8>> for VcfVar { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | = help: `impl From<Local> for Foreign` is allowed by the orphan rules, for more information see https://doc.rust-lang.org/reference/items/implementations.html#trait-implementation-coherence = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#from_over_into = note: `#[warn(clippy::from_over_into)]` on by default help: replace the `Into` implentation with `From<db::create::seqvar_freqs::serialized::VcfVar>` | 132 ~ impl From<VcfVar> for Vec<u8> { 133 ~ fn from(val: VcfVar) -> Self { 134 | let mut result = Vec::new(); 135 | 136 ~ result.extend_from_slice(chrom_name_to_key(&val.chrom).as_bytes()); 137 ~ result.extend_from_slice(&val.pos.to_be_bytes()); 138 ~ result.extend_from_slice(val.reference.as_bytes()); 139 | result.push(b'>'); 140 ~ result.extend_from_slice(val.alternative.as_bytes()); | warning: redundant clone --> src/db/create/seqvar_freqs/serialized.rs:165:14 | 165 | chrom.to_string() | ^^^^^^^^^^^^ help: remove this | note: this value is dropped without further use --> src/db/create/seqvar_freqs/serialized.rs:165:9 | 165 | chrom.to_string() | ^^^^^ = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_clone = note: `#[warn(clippy::redundant_clone)]` on by default warning: stripping a prefix manually --> src/db/create/seqvar_freqs/serialized.rs:149:9 | 149 | &name[3..] | ^^^^^^^^^^ | note: the prefix was tested here --> src/db/create/seqvar_freqs/serialized.rs:148:17 | 148 | let chrom = if name.starts_with("chr") { | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_strip = note: `#[warn(clippy::manual_strip)]` on by default help: try using the `strip_prefix` method | 148 ~ let chrom = if let Some(<stripped>) = name.strip_prefix("chr") { 149 ~ <stripped> | warning: redundant slicing of the whole range --> src/db/create/seqvar_freqs/serialized.rs:151:9 | 151 | &name[..] | ^^^^^^^^^ help: use the original value instead: `name` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_slicing = note: `#[warn(clippy::redundant_slicing)]` on by default warning: variables can be used directly in the `format!` string --> src/db/create/seqvar_freqs/serialized.rs:156:9 | 156 | format!(" {}", chrom) | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#uninlined_format_args help: change this to | 156 - format!(" {}", chrom) 156 + format!(" {chrom}") | warning: length comparison to one --> src/db/create/seqvar_freqs/serialized.rs:161:13 | 161 | assert!(chrom.len() >= 1); | ^^^^^^^^^^^^^^^^ help: using `!is_empty` is clearer and more explicit: `!chrom.is_empty()` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero = note: `#[warn(clippy::len_zero)]` on by default warning: variables can be used directly in the `format!` string --> src/db/create/seqvar_freqs/serialized.rs:163:9 | 163 | format!("0{}", chrom) | ^^^^^^^^^^^^^^^^^^^^^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#uninlined_format_args help: change this to | 163 - format!("0{}", chrom) 163 + format!("0{chrom}") | warning: single-character string constant used as pattern --> src/db/create/seqvar_freqs/serialized.rs:172:24 | 172 | if key.starts_with("0") || key.starts_with(" ") { | ^^^ help: try using a `char` instead: `'0'` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern = note: `#[warn(clippy::single_char_pattern)]` on by default warning: single-character string constant used as pattern --> src/db/create/seqvar_freqs/serialized.rs:172:48 | 172 | if key.starts_with("0") || key.starts_with(" ") { | ^^^ help: try using a `char` instead: `' '` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:75:39 | 75 | MultiVcfReader::new(&[&path_gnomad], assembly) | ^^^^^^^^^^^^ help: change this to: `path_gnomad` | = 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 warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:82:39 | 82 | MultiVcfReader::new(&[&path_helix], assembly) | ^^^^^^^^^^^ help: change this to: `path_helix` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: redundant clone --> src/db/create/seqvar_freqs/mod.rs:145:87 | 145 | self.helix_next = self.helix_reader.as_mut().unwrap().pop()?.0.clone(); | ^^^^^^^^ help: remove this | note: this value is dropped without further use --> src/db/create/seqvar_freqs/mod.rs:145:43 | 145 | self.helix_next = self.helix_reader.as_mut().unwrap().pop()?.0.clone(); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_clone warning: redundant clone --> src/db/create/seqvar_freqs/mod.rs:146:89 | 146 | self.gnomad_next = self.gnomad_reader.as_mut().unwrap().pop()?.0.clone(); | ^^^^^^^^ help: remove this | note: this value is dropped without further use --> src/db/create/seqvar_freqs/mod.rs:146:44 | 146 | self.gnomad_next = self.gnomad_reader.as_mut().unwrap().pop()?.0.clone(); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_clone warning: redundant clone --> src/db/create/seqvar_freqs/mod.rs:150:87 | 150 | self.helix_next = self.helix_reader.as_mut().unwrap().pop()?.0.clone(); | ^^^^^^^^ help: remove this | note: this value is dropped without further use --> src/db/create/seqvar_freqs/mod.rs:150:43 | 150 | self.helix_next = self.helix_reader.as_mut().unwrap().pop()?.0.clone(); | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_clone warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:117:38 | 117 | VcfVar::from_vcf(&helix), | ^^^^^^ help: change this to: `helix` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:119:40 | 119 | MtCounts::from_vcf(&helix), | ^^^^^^ help: change this to: `helix` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:125:38 | 125 | VcfVar::from_vcf(&gnomad), | ^^^^^^^ help: change this to: `gnomad` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:126:40 | 126 | MtCounts::from_vcf(&gnomad), | ^^^^^^^ help: change this to: `gnomad` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:136:61 | 136 | func(var_gnomad, MtCounts::from_vcf(&gnomad), MtCounts::default())?; | ^^^^^^^ help: change this to: `gnomad` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:142:48 | 142 | ... MtCounts::from_vcf(&gnomad), | ^^^^^^^ help: change this to: `gnomad` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:143:48 | 143 | ... MtCounts::from_vcf(&helix), | ^^^^^^ help: change this to: `helix` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: this expression creates a reference which is immediately dereferenced by the compiler --> src/db/create/seqvar_freqs/mod.rs:149:81 | 149 | func(var_helix, MtCounts::default(), MtCounts::from_vcf(&helix))?; | ^^^^^^ help: change this to: `helix` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: the borrowed expression implements the required traits --> src/db/create/seqvar_freqs/mod.rs:184:9 | 184 | &["meta", "nuclear", "mitochondrial"], | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `["meta", "nuclear", "mitochondrial"]` | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow warning: in an `if` condition, avoid complex blocks or closures with blocks; instead, move the block or closure higher and bind it with a `let` --> src/db/create/seqvar_freqs/mod.rs:207:61 | 207 | while mt_reader.run(|variant, gnomad_mtdna, helix_mtdb| { | _____________________________________________________________^ 208 | | tracing::trace!( 209 | | "at {:?} | {:?} | {:?}", 210 | | &variant, ... | 223 | | Ok(()) 224 | | })? { | |_____^ | = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#blocks_in_if_conditions = note: `#[warn(clippy::blocks_in_if_conditions)]` on by default warning: `mehari` (bin "mehari" test) generated 30 warnings ```