[INFO] crate rna-algos 0.1.8 is already in cache
[INFO] extracting crate rna-algos 0.1.8 into work/ex/clippy-test-run/sources/stable/reg/rna-algos/0.1.8
[INFO] extracting crate rna-algos 0.1.8 into work/ex/clippy-test-run/sources/stable+rustflags=-Dclippy%3A%3Ainto_iter_on_array/reg/rna-algos/0.1.8
[INFO] validating manifest of rna-algos-0.1.8 on toolchain stable
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] validating manifest of rna-algos-0.1.8 on toolchain stable+rustflags=-Dclippy::into_iter_on_array
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] started frobbing rna-algos-0.1.8
[INFO] finished frobbing rna-algos-0.1.8
[INFO] frobbed toml for rna-algos-0.1.8 written to work/ex/clippy-test-run/sources/stable/reg/rna-algos/0.1.8/Cargo.toml
[INFO] started frobbing rna-algos-0.1.8
[INFO] finished frobbing rna-algos-0.1.8
[INFO] frobbed toml for rna-algos-0.1.8 written to work/ex/clippy-test-run/sources/stable+rustflags=-Dclippy%3A%3Ainto_iter_on_array/reg/rna-algos/0.1.8/Cargo.toml
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"`
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"`
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] linting rna-algos-0.1.8 against stable for clippy-test-run
[INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/clippy-test-run/worker-0/stable:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/clippy-test-run/sources/stable/reg/rna-algos/0.1.8:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+stable" "clippy" "--frozen" "--all" "--all-targets"`
[INFO] [stdout] a8454d288da9b818a36341904f5762209ac2c3ff27377b2e68e881eed4a61a1c
[INFO] running `"docker" "start" "-a" "a8454d288da9b818a36341904f5762209ac2c3ff27377b2e68e881eed4a61a1c"`
[INFO] [stderr]    Compiling ndarray v0.9.1
[INFO] [stderr]    Compiling bv v0.7.4
[INFO] [stderr]     Checking bio-seq-algos v0.1.11
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking multimap v0.4.0
[INFO] [stderr]     Checking vec_map v0.8.1
[INFO] [stderr]     Checking csv v1.0.5
[INFO] [stderr]     Checking rna-ss-params v0.1.13
[INFO] [stderr]     Checking bio v0.20.3
[INFO] [stderr]     Checking rna-algos v0.1.8 (/opt/crater/workdir)
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/utils.rs:215:7
[INFO] [stderr]     |
[INFO] [stderr] 215 |       fasta_id: fasta_id,
[INFO] [stderr]     |       ^^^^^^^^^^^^^^^^^^ help: replace it with: `fasta_id`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::redundant_field_names)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/utils.rs:216:7
[INFO] [stderr]     |
[INFO] [stderr] 216 |       seq: seq,
[INFO] [stderr]     |       ^^^^^^^^ help: replace it with: `seq`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/utils.rs:215:7
[INFO] [stderr]     |
[INFO] [stderr] 215 |       fasta_id: fasta_id,
[INFO] [stderr]     |       ^^^^^^^^^^^^^^^^^^ help: replace it with: `fasta_id`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::redundant_field_names)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]    --> src/utils.rs:216:7
[INFO] [stderr]     |
[INFO] [stderr] 216 |       seq: seq,
[INFO] [stderr]     |       ^^^^^^^^ help: replace it with: `seq`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: this argument is passed by reference, but would be more efficient if passed by value
[INFO] [stderr]    --> src/utils.rs:222:25
[INFO] [stderr]     |
[INFO] [stderr] 222 | pub fn is_canonical(bp: &BasePair) -> bool {
[INFO] [stderr]     |                         ^^^^^^^^^ help: consider passing by value instead: `BasePair`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::trivially_copy_pass_by_ref)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#trivially_copy_pass_by_ref
[INFO] [stderr] 
[INFO] [stderr] warning: redundant pattern matching, consider using `is_some()`
[INFO] [stderr]    --> src/utils.rs:223:3
[INFO] [stderr]     |
[INFO] [stderr] 223 | /   match CANONICAL_BPS.get(bp) {
[INFO] [stderr] 224 | |     Some(_) => true,
[INFO] [stderr] 225 | |     None => false
[INFO] [stderr] 226 | |   }
[INFO] [stderr]     | |___^ help: try this: `CANONICAL_BPS.get(bp).is_some()`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::redundant_pattern_matching)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_pattern_matching
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/utils.rs:231:17
[INFO] [stderr]     |
[INFO] [stderr] 231 |   let hl = &seq[pp_closing_loop.0 .. pp_closing_loop.1 + 1];
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `pp_closing_loop.0..=pp_closing_loop.1`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::range_plus_one)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: this argument is passed by reference, but would be more efficient if passed by value
[INFO] [stderr]    --> src/utils.rs:322:22
[INFO] [stderr]     |
[INFO] [stderr] 322 | pub fn invert_bp(bp: &BasePair) -> BasePair {(bp.1, bp.0)}
[INFO] [stderr]     |                      ^^^^^^^^^ help: consider passing by value instead: `BasePair`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#trivially_copy_pass_by_ref
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]   --> src/mccaskill_algo.rs:34:33
[INFO] [stderr]    |
[INFO] [stderr] 34 | pub fn get_bpp_mat(log_bpp_mat: &LogProbMat) -> ProbMat {
[INFO] [stderr]    |                                 ^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: the loop variable `i` is used to index `nbpps`
[INFO] [stderr]   --> src/mccaskill_algo.rs:52:12
[INFO] [stderr]    |
[INFO] [stderr] 52 |   for i in 0 .. seq_len {
[INFO] [stderr]    |            ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::needless_range_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_range_loop
[INFO] [stderr] help: consider using an iterator
[INFO] [stderr]    |
[INFO] [stderr] 52 |   for (i, <item>) in nbpps.iter_mut().enumerate().take(seq_len) {
[INFO] [stderr]    |       ^^^^^^^^^^^    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: the function has a cyclomatic complexity of 38
[INFO] [stderr]    --> src/mccaskill_algo.rs:68:1
[INFO] [stderr]     |
[INFO] [stderr] 68  | / pub fn get_log_ss_ppf_mats(seq: SeqSlice, seq_len: usize) -> LogSsPpfMats {
[INFO] [stderr] 69  | |   let mut log_ss_ppf_mats = LogSsPpfMats::new(seq_len);
[INFO] [stderr] 70  | |   for sub_seq_len in MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL .. seq_len + 1 {
[INFO] [stderr] 71  | |     for i in 0 .. seq_len - sub_seq_len + 1 {
[INFO] [stderr] ...   |
[INFO] [stderr] 169 | |   log_ss_ppf_mats
[INFO] [stderr] 170 | | }
[INFO] [stderr]     | |_^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::cyclomatic_complexity)] on by default
[INFO] [stderr]     = help: you could split it up into multiple smaller functions
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cyclomatic_complexity
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]   --> src/mccaskill_algo.rs:70:22
[INFO] [stderr]    |
[INFO] [stderr] 70 |   for sub_seq_len in MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL .. seq_len + 1 {
[INFO] [stderr]    |                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL..=seq_len`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]   --> src/mccaskill_algo.rs:71:14
[INFO] [stderr]    |
[INFO] [stderr] 71 |     for i in 0 .. seq_len - sub_seq_len + 1 {
[INFO] [stderr]    |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `0..=seq_len - sub_seq_len`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:103:10
[INFO] [stderr]     |
[INFO] [stderr] 103 |       if eps_of_terms_4_log_pf.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_pf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::len_zero)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/mccaskill_algo.rs:108:16
[INFO] [stderr]     |
[INFO] [stderr] 108 |       for k in i + 1 .. j + 1 {
[INFO] [stderr]     |                ^^^^^^^^^^^^^^ help: use: `i + 1..=j`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:127:10
[INFO] [stderr]     |
[INFO] [stderr] 127 |       if eps_of_terms_4_log_pf.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_pf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:164:10
[INFO] [stderr]     |
[INFO] [stderr] 164 |       if eps_of_terms_4_log_pf.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_pf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: the function has a cyclomatic complexity of 38
[INFO] [stderr]    --> src/mccaskill_algo.rs:173:1
[INFO] [stderr]     |
[INFO] [stderr] 173 | / fn get_log_base_pairing_prob_mat(seq: SeqSlice, log_ss_ppf_mats: &LogSsPpfMats, seq_len: usize) -> LogProbMat {
[INFO] [stderr] 174 | |   let log_ss_ppf = log_ss_ppf_mats.log_ss_ppf_mat[0][seq_len - 1];
[INFO] [stderr] 175 | |   let mut log_bpp_mat = vec![vec![NEG_INFINITY; seq_len]; seq_len];
[INFO] [stderr] 176 | |   let mut log_prob_mat_4_mls_1 = log_bpp_mat.clone();
[INFO] [stderr] ...   |
[INFO] [stderr] 275 | |   log_bpp_mat
[INFO] [stderr] 276 | | }
[INFO] [stderr]     | |_^
[INFO] [stderr]     |
[INFO] [stderr]     = help: you could split it up into multiple smaller functions
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cyclomatic_complexity
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/mccaskill_algo.rs:178:22
[INFO] [stderr]     |
[INFO] [stderr] 178 |   for sub_seq_len in (MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL .. seq_len + 1).rev() {
[INFO] [stderr]     |                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `(MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL..=seq_len)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/mccaskill_algo.rs:179:14
[INFO] [stderr]     |
[INFO] [stderr] 179 |     for i in 0 .. seq_len - sub_seq_len + 1 {
[INFO] [stderr]     |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `0..=seq_len - sub_seq_len`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:205:10
[INFO] [stderr]     |
[INFO] [stderr] 205 |       if eps_of_terms_4_log_prob_1.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_prob_1.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:208:10
[INFO] [stderr]     |
[INFO] [stderr] 208 |       if eps_of_terms_4_log_prob_2.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_prob_2.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:270:10
[INFO] [stderr]     |
[INFO] [stderr] 270 |       if eps_of_terms_4_log_prob.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_prob.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: this argument is passed by reference, but would be more efficient if passed by value
[INFO] [stderr]    --> src/utils.rs:222:25
[INFO] [stderr]     |
[INFO] [stderr] 222 | pub fn is_canonical(bp: &BasePair) -> bool {
[INFO] [stderr]     |                         ^^^^^^^^^ help: consider passing by value instead: `BasePair`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::trivially_copy_pass_by_ref)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#trivially_copy_pass_by_ref
[INFO] [stderr] 
[INFO] [stderr] warning: redundant pattern matching, consider using `is_some()`
[INFO] [stderr]    --> src/utils.rs:223:3
[INFO] [stderr]     |
[INFO] [stderr] 223 | /   match CANONICAL_BPS.get(bp) {
[INFO] [stderr] 224 | |     Some(_) => true,
[INFO] [stderr] 225 | |     None => false
[INFO] [stderr] 226 | |   }
[INFO] [stderr]     | |___^ help: try this: `CANONICAL_BPS.get(bp).is_some()`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::redundant_pattern_matching)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_pattern_matching
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/utils.rs:231:17
[INFO] [stderr]     |
[INFO] [stderr] 231 |   let hl = &seq[pp_closing_loop.0 .. pp_closing_loop.1 + 1];
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `pp_closing_loop.0..=pp_closing_loop.1`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::range_plus_one)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: this argument is passed by reference, but would be more efficient if passed by value
[INFO] [stderr]    --> src/utils.rs:322:22
[INFO] [stderr]     |
[INFO] [stderr] 322 | pub fn invert_bp(bp: &BasePair) -> BasePair {(bp.1, bp.0)}
[INFO] [stderr]     |                      ^^^^^^^^^ help: consider passing by value instead: `BasePair`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#trivially_copy_pass_by_ref
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]   --> src/mccaskill_algo.rs:34:33
[INFO] [stderr]    |
[INFO] [stderr] 34 | pub fn get_bpp_mat(log_bpp_mat: &LogProbMat) -> ProbMat {
[INFO] [stderr]    |                                 ^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: the loop variable `i` is used to index `nbpps`
[INFO] [stderr]   --> src/mccaskill_algo.rs:52:12
[INFO] [stderr]    |
[INFO] [stderr] 52 |   for i in 0 .. seq_len {
[INFO] [stderr]    |            ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::needless_range_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_range_loop
[INFO] [stderr] help: consider using an iterator
[INFO] [stderr]    |
[INFO] [stderr] 52 |   for (i, <item>) in nbpps.iter_mut().enumerate().take(seq_len) {
[INFO] [stderr]    |       ^^^^^^^^^^^    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: the function has a cyclomatic complexity of 38
[INFO] [stderr]    --> src/mccaskill_algo.rs:68:1
[INFO] [stderr]     |
[INFO] [stderr] 68  | / pub fn get_log_ss_ppf_mats(seq: SeqSlice, seq_len: usize) -> LogSsPpfMats {
[INFO] [stderr] 69  | |   let mut log_ss_ppf_mats = LogSsPpfMats::new(seq_len);
[INFO] [stderr] 70  | |   for sub_seq_len in MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL .. seq_len + 1 {
[INFO] [stderr] 71  | |     for i in 0 .. seq_len - sub_seq_len + 1 {
[INFO] [stderr] ...   |
[INFO] [stderr] 169 | |   log_ss_ppf_mats
[INFO] [stderr] 170 | | }
[INFO] [stderr]     | |_^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::cyclomatic_complexity)] on by default
[INFO] [stderr]     = help: you could split it up into multiple smaller functions
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cyclomatic_complexity
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]   --> src/mccaskill_algo.rs:70:22
[INFO] [stderr]    |
[INFO] [stderr] 70 |   for sub_seq_len in MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL .. seq_len + 1 {
[INFO] [stderr]    |                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL..=seq_len`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]   --> src/mccaskill_algo.rs:71:14
[INFO] [stderr]    |
[INFO] [stderr] 71 |     for i in 0 .. seq_len - sub_seq_len + 1 {
[INFO] [stderr]    |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `0..=seq_len - sub_seq_len`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:103:10
[INFO] [stderr]     |
[INFO] [stderr] 103 |       if eps_of_terms_4_log_pf.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_pf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::len_zero)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/mccaskill_algo.rs:108:16
[INFO] [stderr]     |
[INFO] [stderr] 108 |       for k in i + 1 .. j + 1 {
[INFO] [stderr]     |                ^^^^^^^^^^^^^^ help: use: `i + 1..=j`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:127:10
[INFO] [stderr]     |
[INFO] [stderr] 127 |       if eps_of_terms_4_log_pf.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_pf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:164:10
[INFO] [stderr]     |
[INFO] [stderr] 164 |       if eps_of_terms_4_log_pf.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_pf.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: the function has a cyclomatic complexity of 38
[INFO] [stderr]    --> src/mccaskill_algo.rs:173:1
[INFO] [stderr]     |
[INFO] [stderr] 173 | / fn get_log_base_pairing_prob_mat(seq: SeqSlice, log_ss_ppf_mats: &LogSsPpfMats, seq_len: usize) -> LogProbMat {
[INFO] [stderr] 174 | |   let log_ss_ppf = log_ss_ppf_mats.log_ss_ppf_mat[0][seq_len - 1];
[INFO] [stderr] 175 | |   let mut log_bpp_mat = vec![vec![NEG_INFINITY; seq_len]; seq_len];
[INFO] [stderr] 176 | |   let mut log_prob_mat_4_mls_1 = log_bpp_mat.clone();
[INFO] [stderr] ...   |
[INFO] [stderr] 275 | |   log_bpp_mat
[INFO] [stderr] 276 | | }
[INFO] [stderr]     | |_^
[INFO] [stderr]     |
[INFO] [stderr]     = help: you could split it up into multiple smaller functions
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cyclomatic_complexity
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/mccaskill_algo.rs:178:22
[INFO] [stderr]     |
[INFO] [stderr] 178 |   for sub_seq_len in (MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL .. seq_len + 1).rev() {
[INFO] [stderr]     |                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `(MIN_SPAN_OF_INDEX_PAIR_CLOSING_HL..=seq_len)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/mccaskill_algo.rs:179:14
[INFO] [stderr]     |
[INFO] [stderr] 179 |     for i in 0 .. seq_len - sub_seq_len + 1 {
[INFO] [stderr]     |              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use: `0..=seq_len - sub_seq_len`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:205:10
[INFO] [stderr]     |
[INFO] [stderr] 205 |       if eps_of_terms_4_log_prob_1.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_prob_1.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:208:10
[INFO] [stderr]     |
[INFO] [stderr] 208 |       if eps_of_terms_4_log_prob_2.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_prob_2.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/mccaskill_algo.rs:270:10
[INFO] [stderr]     |
[INFO] [stderr] 270 |       if eps_of_terms_4_log_prob.len() > 0 {
[INFO] [stderr]     |          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!eps_of_terms_4_log_prob.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: the loop variable `k` is used to index `log_ss_ppf_mat`
[INFO] [stderr]   --> tests/lib.rs:21:16
[INFO] [stderr]    |
[INFO] [stderr] 21 |       for k in i + 1 .. j - 1 {
[INFO] [stderr]    |                ^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::needless_range_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_range_loop
[INFO] [stderr] help: consider using an iterator
[INFO] [stderr]    |
[INFO] [stderr] 21 |       for (k, <item>) in log_ss_ppf_mat.iter().enumerate().take(j - 1).skip(i + 1) {
[INFO] [stderr]    |           ^^^^^^^^^^^    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: Constants have by default a `'static` lifetime
[INFO] [stderr]   --> src/bin/mccaskill.rs:19:27
[INFO] [stderr]    |
[INFO] [stderr] 19 | const BPP_MAT_FILE_NAME: &'static str = "bpp_mats.dat";
[INFO] [stderr]    |                          -^^^^^^^---- help: consider removing `'static`: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::const_static_lifetime)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#const_static_lifetime
[INFO] [stderr] 
[INFO] [stderr] warning: Constants have by default a `'static` lifetime
[INFO] [stderr]   --> src/bin/mccaskill.rs:20:17
[INFO] [stderr]    |
[INFO] [stderr] 20 | const VERSION: &'static str = "0.1.8";
[INFO] [stderr]    |                -^^^^^^^---- help: consider removing `'static`: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#const_static_lifetime
[INFO] [stderr] 
[INFO] [stderr] warning: Constants have by default a `'static` lifetime
[INFO] [stderr]   --> src/bin/mccaskill.rs:19:27
[INFO] [stderr]    |
[INFO] [stderr] 19 | const BPP_MAT_FILE_NAME: &'static str = "bpp_mats.dat";
[INFO] [stderr]    |                          -^^^^^^^---- help: consider removing `'static`: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::const_static_lifetime)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#const_static_lifetime
[INFO] [stderr] 
[INFO] [stderr] warning: Constants have by default a `'static` lifetime
[INFO] [stderr]   --> src/bin/mccaskill.rs:20:17
[INFO] [stderr]    |
[INFO] [stderr] 20 | const VERSION: &'static str = "0.1.8";
[INFO] [stderr]    |                -^^^^^^^---- help: consider removing `'static`: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#const_static_lifetime
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]   --> src/bin/mccaskill.rs:47:23
[INFO] [stderr]    |
[INFO] [stderr] 47 |     let seq = unsafe {from_utf8_unchecked(fasta_record.seq()).to_uppercase().as_bytes().iter().filter(|&&base| {is_rna_base(base)}).map(|&base| {base}).collect()};
[INFO] [stderr]    |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `from_utf8_unchecked(fasta_record.seq()).to_uppercase().as_bytes().iter().filter(|&&base| {is_rna_base(base)}).cloned()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::map_clone)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr] warning: You are using an explicit closure for cloning elements
[INFO] [stderr]   --> src/bin/mccaskill.rs:47:23
[INFO] [stderr]    |
[INFO] [stderr] 47 |     let seq = unsafe {from_utf8_unchecked(fasta_record.seq()).to_uppercase().as_bytes().iter().filter(|&&base| {is_rna_base(base)}).map(|&base| {base}).collect()};
[INFO] [stderr]    |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: Consider calling the dedicated `cloned` method: `from_utf8_unchecked(fasta_record.seq()).to_uppercase().as_bytes().iter().filter(|&&base| {is_rna_base(base)}).cloned()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::map_clone)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#map_clone
[INFO] [stderr] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 25.10s
[INFO] running `"docker" "inspect" "a8454d288da9b818a36341904f5762209ac2c3ff27377b2e68e881eed4a61a1c"`
[INFO] running `"docker" "rm" "-f" "a8454d288da9b818a36341904f5762209ac2c3ff27377b2e68e881eed4a61a1c"`
[INFO] [stdout] a8454d288da9b818a36341904f5762209ac2c3ff27377b2e68e881eed4a61a1c