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Store transposed transition matrix to speed up forward #133

Store transposed transition matrix to speed up forward

Store transposed transition matrix to speed up forward #133

Triggered via pull request September 28, 2024 07:11
Status Failure
Total duration 12m 34s
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3 errors, 2 warnings, and 1 notice
Documentation: ../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/examples/interfaces.md:229-232 ```@example interfaces prior_hmm_est, prior_logl_evolution = baum_welch(prior_hmm_guess, obs_seq) first(prior_logl_evolution), last(prior_logl_evolution) ``` exception = TaskFailedException nested task error: MethodError: no method matching transpose_transition_matrix(::Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}) Closest candidates are: transpose_transition_matrix(::AbstractHMM, !Matched::Nothing) @ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/types/abstract_hmm.jl:115 transpose_transition_matrix(::AbstractHMM, !Matched::Any) @ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/types/abstract_hmm.jl:78 transpose_transition_matrix(!Matched::HMM) @ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/types/hmm.jl:67 Stacktrace: [1] transpose_transition_matrix(hmm::Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, ::Nothing) @ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/types/abstract_hmm.jl:115 [2] forward!(storage::HiddenMarkovModels.ForwardBackwardStorage{Float64, Matrix{Float64}}, hmm::Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, obs_seq::Vector{Main.__atexample__named__interfaces.Stuff{Float64}}, control_seq::FillArrays.Fill{Nothing, 1, Tuple{Base.OneTo{Int64}}}, t1::Int64, t2::Int64) @ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/inference/forward.jl:73 [3] forward_backward!(storage::HiddenMarkovModels.ForwardBackwardStorage{Float64, Matrix{Float64}}, hmm::Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, obs_seq::Vector{Main.__atexample__named__interfaces.Stuff{Float64}}, control_seq::FillArrays.Fill{Nothing, 1, Tuple{Base.OneTo{Int64}}}, t1::Int64, t2::Int64; transition_marginals::Bool) @ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/inference/forward_backward.jl:72 [4] forward_backward! @ ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/inference/forward_backward.jl:60 [inlined] [5] macro expansion @ ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/inference/forward_backward.jl:113 [inlined] [6] (::HiddenMarkovModels.var"#131#threadsfor_fun#17"{HiddenMarkovModels.var"#131#threadsfor_fun#16#18"{FillArrays.Fill{Int64, 1, Tuple{Base.OneTo{Int64}}}, Bool, HiddenMarkovModels.ForwardBackwardStorage{Float64, Matrix{Float64}}, Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, Vector{Main.__atexample__named__interfaces.Stuff{Float64}}, FillArrays.Fill{Nothing, 1, Tuple{Base.OneTo{Int64}}}, Vector{Float64}, Base.OneTo{Int64}}})(tid::Int64; onethread::Bool) @ HiddenMarkovModels ./threadingconstructs.jl:215 [7] #131#threadsfor_fun @ ./threadingconstructs.jl:182 [inlined] [8] (::Base.Threads.var"#1#2"{HiddenMarkovModels.var"#131#threadsfor_fun#17"{HiddenMarkovModels.var"#131#threadsfor_fun#16#18"{FillArrays.Fill{Int64, 1, Tuple{Base.OneTo{Int64}}}, Bool, HiddenMarkovModels.ForwardBackwardStorage{Float64, Matrix{Float64}}, Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, Vector{Main.__atexample__named__interfaces.Stuff{Float64}}, FillArrays.Fill{Nothing, 1, Tuple{Base.OneTo{Int64}}}, Vector{Float64}, Base.OneTo{Int64}}}, Int64})() @ Base.Threads ./threadingconstructs.jl:154 Stacktrace: [1] threading_run(fun::HiddenMarkovModels.var"#131#threadsfor_fun#17"{HiddenMarkovModels.var"#131#threadsfor_fun#16#18"{FillArrays.Fill{Int64, 1, Tuple{Base
Documentation: ../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/examples/interfaces.md:236-238 ```@example interfaces cat(transition_matrix(hmm_est), transition_matrix(prior_hmm_est); dims=3) ``` exception = UndefVarError: `prior_hmm_est` not defined Stacktrace: [1] top-level scope @ interfaces.md:237 [2] eval @ ./boot.jl:385 [inlined] [3] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
Documentation
Process completed with exit code 1.
Documentation
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Documentation
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[julia-buildpkg] Caching of the julia depot was not detected
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