cargo : warning: unused variable: `matrix`
At line:1 char:1
+ cargo test --lib --release > test_kernel_final.txt 2>&1; (Get-Content ...
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : NotSpecified: (warning: unused variable: `matrix 
   `:String) [], RemoteException
    + FullyQualifiedErrorId : NativeCommandError
 
   --> src\alignment\kernel_launcher.rs:123:9
    |
123 |         matrix: &[i32],
    |         ^^^^^^ help: if this is intentional, prefix it with an 
underscore: `_matrix`
    |
    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by 
default

warning: unused variable: `gap_open`
   --> src\alignment\kernel_launcher.rs:124:9
    |
124 |         gap_open: i32,
    |         ^^^^^^^^ help: if this is intentional, prefix it with an 
underscore: `_gap_open`

warning: unused variable: `gap_extend`
   --> src\alignment\kernel_launcher.rs:125:9
    |
125 |         gap_extend: i32,
    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an 
underscore: `_gap_extend`

warning: variable does not need to be mutable
   --> src\alignment\hmmer3_parser.rs:588:13
    |
588 |         let mut model = HmmerModel {
    |             ----^^^^^
    |             |
    |             help: remove this `mut`
    |
    = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default

warning: variable does not need to be mutable
    --> src\alignment\simd_viterbi.rs:1082:13
     |
1082 |         let mut decoder = ViterbiDecoder::new_dummy();
     |             ----^^^^^^^
     |             |
     |             help: remove this `mut`

warning: unused variable: `a2`
   --> src\alignment\gpu_memory.rs:343:13
    |
343 |         let a2 = pool.allocate(1000).unwrap();
    |             ^^ help: if this is intentional, prefix it with an 
underscore: `_a2`

warning: unused variable: `backend`
   --> src\futures\gpu_jit_compiler.rs:111:23
    |
111 |     fn verify_backend(backend: GpuBackend) -> Result<()> {
    |                       ^^^^^^^ help: if this is intentional, prefix it 
with an underscore: `_backend`

warning: associated function `compute_sw_cpu` is never used
   --> src\alignment\kernel_launcher.rs:120:8
    |
 40 | impl SmithWatermanKernel {
    | ------------------------ associated function in this implementation
...
120 |     fn compute_sw_cpu(
    |        ^^^^^^^^^^^^^^
    |
    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default

warning: associated function `compute_nw_cpu` is never used
   --> src\alignment\kernel_launcher.rs:254:8
    |
180 | impl NeedlemanWunschKernel {
    | -------------------------- associated function in this implementation
...
254 |     fn compute_nw_cpu(
    |        ^^^^^^^^^^^^^^

warning: associated function `execute_viterbi_kernel` is never used
   --> src\alignment\simd_viterbi.rs:309:8
    |
 61 | impl ViterbiDecoder {
    | ------------------- associated function in this implementation
...
309 |     fn execute_viterbi_kernel(
    |        ^^^^^^^^^^^^^^^^^^^^^^

warning: comparison is useless due to type limits
   --> src\futures\tree_refinement.rs:297:17
    |
297 |         assert!(improvements >= 0);
    |                 ^^^^^^^^^^^^^^^^^
    |
    = note: `#[warn(unused_comparisons)]` on by default

warning: comparison is useless due to type limits
   --> src\futures\tree_refinement.rs:328:17
    |
328 |         assert!(improvements >= 0);
    |                 ^^^^^^^^^^^^^^^^^

warning: comparison is useless due to type limits
   --> src\futures\tree_refinement.rs:360:17
    |
360 |         assert!(improvements >= 0);
    |                 ^^^^^^^^^^^^^^^^^

warning: comparison is useless due to type limits
   --> src\futures\phylogeny_parsimony.rs:377:17
    |
377 |         assert!(cost >= 0);
    |                 ^^^^^^^^^

warning: `omics-simd` (lib test) generated 14 warnings (run `cargo fix --lib 
-p omics-simd --tests` to apply 7 suggestions)
    Finished `release` profile [optimized] target(s) in 0.07s
     Running unittests src\lib.rs 
(target\release\deps\omics_simd-e10d7ebebde719eb.exe)

running 248 tests
test alignment::bam::tests::test_bam_file_creation ... ok
test alignment::bam::tests::test_invalid_utf8_in_read_name ... ok
test alignment::bam::tests::test_cigar_formatting ... ok
test alignment::bam::tests::test_bam_serialization ... ok
test alignment::bam::tests::test_sequence_encoding ... ok
test alignment::cuda_kernels::tests::test_multi_gpu_batch ... ok
test alignment::bam::tests::test_cigar_parsing ... ok
test alignment::gpu_dispatcher::tests::test_gpu_memory_estimation ... ok
test alignment::bam::tests::test_invalid_utf8_in_bam_header ... ok
test alignment::cigar_gen::tests::test_cigar_generation ... ok
test alignment::cigar_gen::tests::test_cigar_lengths ... ok
test alignment::gpu_memory::tests::test_fragmentation ... ok
test alignment::cuda_kernels::tests::test_cuda_compute_capability ... ok
test alignment::cuda_kernels::tests::test_grid_calculation ... ok
test alignment::batch::tests::test_batch_with_bandwidth ... ok
test alignment::cuda_runtime::tests::test_device_detection ... ok
test alignment::batch::tests::test_batch_smith_waterman ... ok
test alignment::batch::tests::test_batch_needleman_wunsch ... ok
test alignment::batch::tests::test_batch_filter_by_score ... ok
test alignment::gpu_dispatcher::tests::test_gpu_dispatcher_creation ... ok
test alignment::gpu_dispatcher::tests::test_optimization_hints ... ok
test alignment::gpu_dispatcher::tests::test_speedup_factors ... ok
test alignment::gpu_kernels::tests::test_gpu_config_default ... ok
test alignment::gpu_kernels::tests::test_memory_pool ... ok
test alignment::gpu_kernels::tests::test_multi_gpu_distribution ... ok
test alignment::cigar_gen::tests::test_cigar_parsing ... ok
test alignment::cigar_gen::tests::test_hmm_cigar_generation ... ok
test alignment::cuda_kernels::tests::test_kernel_config ... ok
test alignment::bam::tests::test_invalid_utf8_in_reference_name ... ok
test alignment::cuda_kernels::tests::test_shared_memory_size ... ok
test alignment::cuda_kernels::tests::test_time_estimation ... ok
test alignment::gpu_dispatcher::tests::test_alignment_strategy_selection ... ok
test alignment::bam::tests::test_valid_utf8_roundtrip ... ok
test alignment::gpu_memory::tests::test_host_device_transfer ... ok
test alignment::gpu_memory::tests::test_memory_deallocation ... ok
test alignment::gpu_memory::tests::test_memory_pool_allocation ... ok
test alignment::gpu_memory::tests::test_multilevel_gpu_memory ... ok
test alignment::hmmer3_parser::tests::test_evalue_calculation ... ok
test alignment::hmmer3_parser::tests::test_hmmer_model_creation ... ok
test alignment::hmmer3_parser::tests::test_hmmer_model_null_model_normalization ... ok
test alignment::hmmer3_parser::tests::test_karlin_evalue_bounds ... ok
test alignment::hmmer3_parser::tests::test_karlin_parameters ... ok
test alignment::hmmer3_parser::tests::test_parse_error_invalid_numeric_score ... ok
test alignment::hmmer3_parser::tests::test_parse_error_special_scores ... ok
test alignment::kernel::avx2::tests::test_avx2_smith_waterman_fallback ... ok
test alignment::kernel::banded::tests::test_banded_fallback_different_lengths ... ok
test alignment::kernel::banded::tests::test_banded_nw_similar_sequences ... ok
test alignment::kernel::banded::tests::test_banded_sw_similar_sequences ... ok
test alignment::hmmer3_parser::tests::test_regex_compilation_safety ... ok
test alignment::kernel::hmm_simd::tests::test_baum_welch_convergence ... ok
test alignment::kernel::hmm_simd::tests::test_backward_algorithm ... ok
test alignment::kernel::hmm_simd::tests::test_baum_welch_iteration ... ok
test alignment::kernel::hmm_simd::tests::test_empty_sequence_error ... ok
test alignment::kernel::hmm_simd::tests::test_forward_algorithm ... ok
test alignment::kernel::hmm_simd::tests::test_forward_backward_consistency ... ok
test alignment::kernel::hmm_simd::tests::test_forward_score_range ... ok
test alignment::kernel::hmm_simd::tests::test_logsumexp_extreme_values ... ok
test alignment::kernel::hmm_simd::tests::test_logsumexp_stability ... ok
test alignment::kernel::hmm_simd::tests::test_logsumexp_zero_values ... ok
test alignment::kernel::hmm_simd::tests::test_long_sequence ... ok
test alignment::kernel::hmm_simd::tests::test_multiple_sequence_alignment ... ok
test alignment::kernel::hmm_simd::tests::test_single_amino_acid ... ok
test alignment::kernel::hmm_simd::tests::test_viterbi_all_amino_acids ... ok
test alignment::kernel::hmm_simd::tests::test_viterbi_backtrack ... ok
test alignment::kernel::hmm_simd::tests::test_viterbi_different_paths ... ok
test alignment::kernel::hmm_simd::tests::test_viterbi_simple ... ok
test alignment::kernel::msa_simd::tests::test_batch_profile_scoring ... ok
test alignment::kernel::msa_simd::tests::test_dirichlet_prior ... ok
test alignment::kernel::msa_simd::tests::test_dirichlet_prior_application ... ok
test alignment::kernel::msa_simd::tests::test_edge_case_invalid_alignment ... ok
test alignment::kernel::msa_simd::tests::test_edge_case_invalid_background ... ok
test alignment::kernel::msa_simd::tests::test_empty_alignment_error ... ok
test alignment::kernel::msa_simd::tests::test_entropy_computation ... ok
test alignment::kernel::msa_simd::tests::test_entropy_conservation ... ok
test alignment::kernel::msa_simd::tests::test_entropy_divergence ... ok
test alignment::kernel::msa_simd::tests::test_henikoff_weights ... ok
test alignment::kernel::msa_simd::tests::test_kl_divergence ... ok
test alignment::kernel::msa_simd::tests::test_long_alignment ... ok
test alignment::kernel::msa_simd::tests::test_profile_alignment_multiple_sequences ... ok
test alignment::kernel::msa_simd::tests::test_profile_scoring ... ok
test alignment::kernel::msa_simd::tests::test_pssm_construction ... ok
test alignment::kernel::msa_simd::tests::test_pssm_diverse_alignment ... ok
test alignment::kernel::msa_simd::tests::test_pssm_identical_sequences ... ok
test alignment::kernel::msa_simd::tests::test_pssm_score_range ... ok
test alignment::kernel::msa_simd::tests::test_pssm_single_sequence ... ok
test alignment::kernel::msa_simd::tests::test_score_frequency ... ok
test alignment::kernel::scalar::tests::test_smith_waterman_scalar ... ok
test alignment::kernel::striped_simd::tests::test_needleman_wunsch_striped ... ok
test alignment::kernel::striped_simd::tests::test_smith_waterman_striped_empty ... ok
test alignment::kernel::striped_simd::tests::test_smith_waterman_striped_match ... ok
test alignment::kernel::striped_simd::tests::test_smith_waterman_striped_single ... ok
test alignment::kernel::striped_simd::tests::test_striped_vs_scalar_consistency ... ok
test alignment::kernel_compiler::tests::test_kernel_cache ... ok
test alignment::kernel_compiler::tests::test_compiler_creation ... ok
test alignment::kernel_compiler::tests::test_kernel_type_names ... ok
test alignment::kernel_compiler::tests::test_source_hash ... ok
test alignment::kernel_launcher::tests::test_kernel_launcher_without_cuda ... ok
test alignment::profile_dp::tests::test_profile_alignment ... ok
test alignment::profile_dp::tests::test_profile_similarity ... ok
test alignment::profile_dp::tests::test_pssm_creation ... ok
test alignment::simd_viterbi::tests::test_backtrack_generation ... ok
test alignment::simd_viterbi::tests::test_decoder_has_gpu_field ... ok
test alignment::simd_viterbi::tests::test_gpu_dispatcher_initialization ... ok
test alignment::simd_viterbi::tests::test_viterbi_decoder_creation ... ok
test alignment::tests::test_alignment_cigar_generation ... ok
test alignment::tests::test_alignment_result_identity ... ok
test alignment::tests::test_cigar_coalesce ... ok
test alignment::tests::test_cigar_lengths ... ok
test alignment::tests::test_cigar_operations ... ok
test alignment::tests::test_sam_header_generation ... ok
test alignment::tests::test_sam_record_creation ... ok
test alignment::tests::test_sam_record_from_alignment ... ok
test alignment::tests::test_sam_record_to_line ... ok
test alignment::tests::test_smith_waterman ... ok
test alignment::tests::test_smith_waterman_with_cigar ... ok
test futures::cli_file_io::tests::test_batch_processor_creation ... ok
test futures::cli_file_io::tests::test_batch_processor_with_filter ... ok
test futures::cli_file_io::tests::test_file_format_detection ... ok
test futures::cli_file_io::tests::test_parse_fasta_header ... ok
test futures::cli_file_io::tests::test_parse_fastq_header ... ok
test futures::cli_file_io::tests::test_seq_record_creation ... ok
test futures::cli_file_io::tests::test_seq_record_header ... ok
test futures::formats::tests::test_blast_json_export ... ok
test futures::formats::tests::test_blast_json_to_tabular ... ok
test futures::formats::tests::test_blast_tabular_export ... ok
test futures::formats::tests::test_blast_xml_export ... ok
test futures::formats::tests::test_fasta_export ... ok
test futures::formats::tests::test_fasta_wrapping ... ok
test futures::formats::tests::test_gff3_invalid_coordinates ... ok
test futures::formats::tests::test_gff3_line_format ... ok
test futures::formats::tests::test_gff3_record_creation ... ok
test futures::gpu::tests::test_cuda_device_creation ... ok
test futures::gpu::tests::test_cuda_device_detection ... ok
test futures::gpu::tests::test_data_transfer_size_mismatch ... ok
test futures::gpu::tests::test_data_transfer_to_gpu ... ok
test futures::gpu::tests::test_device_creation_produces_unique_ids ... ok
test futures::gpu::tests::test_gpu_memory_allocation ... ok
test futures::gpu::tests::test_gpu_memory_zero_allocation ... ok
test futures::gpu::tests::test_hip_device_creation ... ok
test futures::gpu::tests::test_needleman_wunsch_gpu_kernel ... ignored
test futures::gpu::tests::test_multi_gpu_execution ... ok
test futures::gpu::tests::test_multiple_memory_allocations ... ok
test futures::gpu::tests::test_smith_waterman_gpu_kernel ... ignored
test futures::hmmer3_full_parser::tests::test_database_lookup ... ok
test futures::gpu::tests::test_vulkan_device_creation ... ok
test futures::gpu_jit_compiler::tests::test_cache_key_generation ... ok
test futures::gpu_jit_compiler::tests::test_compilation_options ... ok
test futures::gpu_jit_compiler::tests::test_jit_compiler_creation ... ok
test futures::gpu_jit_compiler::tests::test_kernel_templates ... ok
test futures::hmm::tests::test_domain_detection ... ok
test futures::hmm::tests::test_baum_welch_training ... ok
test futures::hmm::tests::test_evalue_computation ... ok
test futures::hmm::tests::test_forward_algorithm ... ok
test futures::hmm::tests::test_hmm_from_msa ... ok
test futures::hmm::tests::test_pfam_loading ... ok
test futures::hmm::tests::test_viterbi_algorithm ... ok
test futures::hmmer3_full_parser::tests::test_database_insertion ... ok
test futures::hmmer3_full_parser::tests::test_emission_matrix_parsing ... ok
test futures::hmmer3_full_parser::tests::test_hmmer3_database_creation ... ok
test futures::hmmer3_full_parser::tests::test_model_creation ... ok
test futures::hmm::tests::test_backward_algorithm ... ok
test futures::hmmer3_full_parser::tests::test_model_names ... ok
test futures::hmmer3_full_parser::tests::test_pssm_generation ... ok
test futures::hmmer3_full_parser::tests::test_threshold_checking ... ok
test futures::hmm::tests::test_forward_backward ... ok
test futures::gpu::tests::test_smith_waterman_empty_sequences ... ok
test futures::matrices::tests::test_gonnet_loading ... ok
test futures::matrices::tests::test_hoxd_variants ... ok
test futures::matrices::tests::test_invalid_matrix_dimensions ... ok
test futures::matrices::tests::test_matrix_symmetry_pam40 ... ok
test futures::matrices::tests::test_matrix_validation_gonnet ... ok
test futures::matrices::tests::test_matrix_validation_pam70 ... ok
test futures::matrices::tests::test_pam40_loading ... ok
test futures::matrices::tests::test_pam70_loading ... ok
test futures::matrices::tests::test_pam_variant_loading ... ok
test futures::msa::tests::test_align_to_profile ... ok
test futures::msa::tests::test_consensus_generation ... ok
test futures::msa::tests::test_conservation_scoring ... ok
test futures::msa::tests::test_guide_tree_construction ... ok
test futures::msa::tests::test_distance_matrix_computation ... ok
test futures::msa::tests::test_profile_building ... ok
test futures::msa::tests::test_progressive_msa ... ok
test futures::msa_profile_alignment::tests::test_consensus_computation ... ok
test futures::msa_profile_alignment::tests::test_gap_identification ... ok
test futures::msa_profile_alignment::tests::test_henikoff_weights ... ok
test futures::msa_profile_alignment::tests::test_pipeline_creation ... ok
test futures::msa_profile_alignment::tests::test_profile_to_profile_alignment ... ok
test futures::msa_profile_alignment::tests::test_profile_to_sequence_alignment ... ok
test futures::pfam::tests::test_bit_score_calculation ... ok
test futures::pfam::tests::test_evalue_calculation ... ok
test futures::pfam::tests::test_evalue_stats_protein ... ok
test futures::pfam::tests::test_pfam_database_creation ... ok
test futures::pfam::tests::test_pvalue_calculation ... ok
test futures::phylogeny::tests::test_ancestral_reconstruction ... ok
test futures::phylogeny::tests::test_bootstrap_analysis ... ok
test futures::phylogeny::tests::test_compute_phylogenetic_distances ... ok
test futures::phylogeny::tests::test_maximum_likelihood ... ok
test futures::phylogeny::tests::test_maximum_parsimony ... ok
test futures::phylogeny::tests::test_neighbor_joining ... ok
test futures::phylogeny::tests::test_newick_format ... ok
test futures::phylogeny::tests::test_rooting_tree ... ok
test futures::phylogeny::tests::test_tree_builder ... ok
test futures::phylogeny::tests::test_tree_statistics ... ok
test futures::phylogeny_likelihood::tests::test_likelihood_builder_creation ... ok
test futures::phylogeny_likelihood::tests::test_nni_convergence ... ok
test futures::phylogeny::tests::test_upgma_tree_building ... ok
test futures::phylogeny_likelihood::tests::test_spr_convergence ... ok
test futures::phylogeny_likelihood::tests::test_topology_search_result_creation ... ok
test futures::phylogeny_likelihood::tests::test_tree_node_creation ... ok
test futures::phylogeny_parsimony::tests::test_ambiguous_states ... ok
test futures::phylogeny_parsimony::tests::test_char_state_creation ... ok
test futures::phylogeny_parsimony::tests::test_char_state_transition ... ok
test futures::phylogeny_parsimony::tests::test_parsimony_scoring ... ok
test futures::phylogeny_parsimony::tests::test_parsimony_tree_builder ... ok
test futures::phylogeny_parsimony::tests::test_state_set_intersection ... ok
test futures::phylogeny_parsimony::tests::test_state_set_union ... ok
test futures::phylogeny_parsimony::tests::test_transition_cost ... ok
test futures::st_jude_bridge::tests::test_alignment_conversion ... ok
test futures::st_jude_bridge::tests::test_bridge_empty_sequence_validation ... ok
test futures::st_jude_bridge::tests::test_bridge_protein_to_st_jude ... ok
test futures::st_jude_bridge::tests::test_clinical_flags ... ok
test futures::st_jude_bridge::tests::test_bridge_st_jude_to_protein ... ok
test futures::st_jude_bridge::tests::test_parsimony_state_creation ... ok
test futures::st_jude_bridge::tests::test_metadata_preservation ... ok
test futures::st_jude_bridge::tests::test_seq_record_to_st_jude ... ok
test futures::st_jude_bridge::tests::test_bridge_roundtrip_conversion ... ok
test futures::st_jude_bridge::tests::test_st_jude_amino_acid_conversion ... ok
test futures::st_jude_bridge::tests::test_taxonomy_id_defaults ... ok
test futures::st_jude_bridge::tests::test_three_letter_codes ... ok
test futures::tree_refinement::tests::test_nni_refinement ... ok
test futures::tree_refinement::tests::test_spr_refinement ... ok
test futures::tree_refinement::tests::test_tree_optimizer ... ok
test protein::tests::test_amino_acid_from_code ... ok
test protein::tests::test_amino_acid_to_code ... ok
test protein::tests::test_protein_creation ... ok
test protein::tests::test_protein_with_metadata ... ok
test scoring::tests::test_affine_penalty ... ok
test scoring::tests::test_blosum45_matrix ... ok
test scoring::tests::test_blosum80_matrix ... ok
test scoring::tests::test_invalid_penalty ... ok
test scoring::tests::test_matrix_symmetry_blosum45 ... ok
test scoring::tests::test_matrix_symmetry_pam70 ... ok
test scoring::tests::test_matrix_type_display ... ok
test scoring::tests::test_pam30_matrix ... ok
test scoring::tests::test_pam70_matrix ... ok
test scoring::tests::test_scoring_matrix ... ok
test futures::gpu::tests::test_gpu_device_properties_non_zero_memory ... ok
test futures::gpu::tests::test_device_properties_name_validated ... ok

test result: ok. 246 passed; 0 failed; 2 ignored; 0 measured; 0 filtered out; finished in 0.72s

