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whale.jl's Issues

how to build Arpack in julia

When I tried installing whale.pj on v1.1.1 and saw this error:

Building Arpack → ~/.julia/packages/Arpack/cu5By/deps/build.log
┌ Error: Error building Arpack:
│ [ Info: Downloading https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-3/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc7.tar.gz
to /home/nieshuai/.julia/packages/Arpack/cu5By/deps/usr/downloads/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc7.tar.gz...
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/home/nieshuai/.julia/packages/Arpack/cu5By/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/nieshuai/.julia/packages/BinaryProvider/TcAwt/src/Products.jl:414
│ [3] (::getfield(BinaryProvider, Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}}, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at ./none:0
│ [4] top-level scope at none:0
│ [5] include at ./boot.jl:326 [inlined]
│ [6] include_relative(::Module, ::String) at ./loading.jl:1038
│ [7] include(::Module, ::String) at ./sysimg.jl:29
│ [8] include(::String) at ./client.jl:403
│ [9] top-level scope at none:0
│ in expression starting at /home/nieshuai/.julia/packages/Arpack/cu5By/deps/build.jl:74
[21:15:25] ######################################################################## 100.0%

the info of julia:
versioninfo()
Julia Version 1.1.1
Platform Info:
OS: Linux (x86_64-conda_cos6-linux-gnu)
CPU: Intel(R) Xeon(R) CPU E5-2630 0 @ 2.30GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-6.0.1 (ORCJIT, sandybridge)

To solve this problem, I used three methods:

  1. I used the official binaries from julialang.org, but the version of my apt-get is too low and the upgrade failed.
  2. I see JuliaLinearAlgebra/Arpack.jl#5. however, I couldn't find an effective way.
  3. Ultimately, I tried the solution suggested by the third answer at https://www.oipapio.com/question-11699618. But I can't find libopenblas64_.so.0 in my system.

Could you give me some advice on how to solve it?

Error to install Whale

Hi,

I am having the issue below to install Whale. Do you know what does it mean? Thank you!

(@v1.5) pkg> add https://github.com/arzwa/Whale.jl
   Updating git-repo `https://github.com/arzwa/Whale.jl`
   Updating registry at `~/.julia/registries/General`
######################################################################## 100.0%
  Resolving package versions...
No Changes to `~/.julia/environments/v1.5/Project.toml`
No Changes to `~/.julia/environments/v1.5/Manifest.toml`

julia> using Whale
[ Info: Precompiling Whale [eab5b8f2-ac71-4eb1-ac2b-64791b8dae63]
WARNING: could not import NewickTree.id into Whale
WARNING: could not import NewickTree.name into Whale
WARNING: could not import NewickTree.distance into Whale
ERROR: LoadError: LoadError: UndefVarError: distance not defined
Stacktrace:
 [1] getproperty(::Module, ::Symbol) at ./Base.jl:26
 [2] top-level scope at /home/ubuntu/.julia/packages/Whale/SZSk2/src/dlsim.jl:13
 [3] include(::Function, ::Module, ::String) at ./Base.jl:380
 [4] include at ./Base.jl:368 [inlined]
 [5] include(::String) at /home/ubuntu/.julia/packages/Whale/SZSk2/src/Whale.jl:1
 [6] top-level scope at /home/ubuntu/.julia/packages/Whale/SZSk2/src/Whale.jl:24
 [7] include(::Function, ::Module, ::String) at ./Base.jl:380
 [8] include(::Module, ::String) at ./Base.jl:368
 [9] top-level scope at none:2
 [10] eval at ./boot.jl:331 [inlined]
 [11] eval(::Expr) at ./client.jl:467
 [12] top-level scope at ./none:3
in expression starting at /home/ubuntu/.julia/packages/Whale/SZSk2/src/dlsim.jl:13
in expression starting at /home/ubuntu/.julia/packages/Whale/SZSk2/src/Whale.jl:24
ERROR: Failed to precompile Whale [eab5b8f2-ac71-4eb1-ac2b-64791b8dae63] to /home/ubuntu/.julia/compiled/v1.5/Whale/4nkxD_q3KDU.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1305
 [3] _require(::Base.PkgId) at ./loading.jl:1030
 [4] require(::Base.PkgId) at ./loading.jl:928
 [5] require(::Module, ::Symbol) at ./loading.jl:923

UndefVarError: hasfield not defined

Hi Arthur,

I am still having problems to run Whale. I have an ultrametric tree and a bunch of ale files (filtered using your scripts). I am trying to infer WGD in the species tree.

I am following the "Reconciled tree inference example" but I was not able to set the model variable following your command:

model = WhaleModel(RatesModel(ConstantDLWGD(λ=0.1, μ=0.2, η=0.9)), tree, .1)`
ERROR: UndefVarError: hasfield not defined
Stacktrace:
 [1] getp(::ConstantDLWGD{Float64,Float64}, ::Node{UInt16,Whale.Slices{Float64,UInt16}}) at /home/ubuntu/.julia/packages/Whale/SZSk2/src/rmodels.jl:21
 [2] getθ(::ConstantDLWGD{Float64,Float64}, ::Node{UInt16,Whale.Slices{Float64,UInt16}}) at /home/ubuntu/.julia/packages/Whale/SZSk2/src/rmodels.jl:54
 [3] getθ at /home/ubuntu/.julia/packages/Whale/SZSk2/src/rmodels.jl:20 [inlined]
 [4] setnode!(::Node{UInt16,Whale.Slices{Float64,UInt16}}, ::RatesModel{Float64,ConstantDLWGD{Float64,Float64},TransformVariables.TransformTuple{NamedTuple{(:λ, :μ, :η, :q, :p),Tuple{TransformVariables.ShiftedExp{true,Float64},TransformVariables.ShiftedExp{true,Float64},TransformVariables.ScaledShiftedLogistic{Float64},TransformVariables.ArrayTransform{TransformVariables.ScaledShiftedLogistic{Float64},1},TransformVariables.ArrayTransform{TransformVariables.ScaledShiftedLogistic{Float64},1}}}}}) at /home/ubuntu/.julia/packages/Whale/SZSk2/src/model.jl:146
 [5] setmodel!(::WhaleModel{Float64,RatesModel{Float64,ConstantDLWGD{Float64,Float64},TransformVariables.TransformTuple{NamedTuple{(:λ, :μ, :η, :q, :p),Tuple{TransformVariables.ShiftedExp{true,Float64},TransformVariables.ShiftedExp{true,Float64},TransformVariables.ScaledShiftedLogistic{Float64},TransformVariables.ArrayTransform{TransformVariables.ScaledShiftedLogistic{Float64},1},TransformVariables.ArrayTransform{TransformVariables.ScaledShiftedLogistic{Float64},1}}}}},UInt16,Whale.RootCondition}) at /home/ubuntu/.julia/packages/Whale/SZSk2/src/model.jl:141
 [6] #WhaleModel#42(::Int64, ::Whale.RootCondition, ::Type, ::RatesModel{Float64,ConstantDLWGD{Float64,Float64},TransformVariables.TransformTuple{NamedTuple{(:λ, :μ, :η, :q, :p),Tuple{TransformVariables.ShiftedExp{true,Float64},TransformVariables.ShiftedExp{true,Float64},TransformVariables.ScaledShiftedLogistic{Float64},TransformVariables.ArrayTransform{TransformVariables.ScaledShiftedLogistic{Float64},1},TransformVariables.ArrayTransform{TransformVariables.ScaledShiftedLogistic{Float64},1}}}}}, ::Node{UInt16,NewickData{Float64,String}}, ::Float64) at /home/ubuntu/.julia/packages/Whale/SZSk2/src/model.jl:120
 [7] WhaleModel(::RatesModel{Float64,ConstantDLWGD{Float64,Float64},TransformVariables.TransformTuple{NamedTuple{(:λ, :μ, :η, :q, :p),Tuple{TransformVariables.ShiftedExp{true,Float64},TransformVariables.ShiftedExp{true,Float64},TransformVariables.ScaledShiftedLogistic{Float64},TransformVariables.ArrayTransform{TransformVariables.ScaledShiftedLogistic{Float64},1},TransformVariables.ArrayTransform{TransformVariables.ScaledShiftedLogistic{Float64},1}}}}}, ::Node{UInt16,NewickData{Float64,String}}, ::Float64) at /home/ubuntu/.julia/packages/Whale/SZSk2/src/model.jl:83
 [8] top-level scope at none:0

Do you know where is the problem?

thank you
Cintia

Threadtools version?

Hi Arthur,

Super curious to use this software. I am having issues with the package of ThreadTools. Any tip to which one is the appropriate one?

Many thanks in advance,
O

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