Error to install Whale

[cintiaiha]

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

[arzwa]

Hi, I cannot reproduce this issue. It seems to have to do something with the NewickTree package, maybe try rm NewickTree Whale and retry adding Whale?

Alternatively, I would recommend trying to install Whale in a fresh project environment and try again. Basically, make a directory whale-env for instance, go to it from your terminal, startup julia, and hit

]activate .

Now try add' Whale` again:

(whale-env) pkg> add https://github.com/arzwa/Whale.jl

It should work after that (it does for me).

[cintiaiha]

Hi Arthur,

Thank you very much for your reply.

It seems that it is working, but I could follow all pipeline yet. I tried many different approached and at the end, I uninstalled Julia from the server (it was installed by apt-get and I had to used sudo every time I startup julia), created a new environment with conda, installed Julia with conda, make a new directory "whale_env", and add Whale again as you suggested:

(whale_env) pkg> add https://github.com/arzwa/Whale.jl
Updating registry at ~/.julia/registries/General
Updating git-repo https://github.com/JuliaRegistries/General.git
Cloning git-repo https://github.com/arzwa/Whale.jl
Updating git-repo https://github.com/arzwa/Whale.jl
Resolving package versions...
Installed Rmath ─────────────────────── v0.6.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed FillArrays ────────────────── v0.9.7
Installed DiffRules ─────────────────── v1.0.1
Installed SpecialFunctions ──────────── v0.8.0
Installed BinDeps ───────────────────── v1.0.1
Installed CategoricalArrays ─────────── v0.8.3
Installed JSON ──────────────────────── v0.21.1
Installed Reexport ──────────────────── v0.2.0
Installed Compat ────────────────────── v3.20.0
Installed InvertedIndices ───────────── v1.0.0
Installed StaticArrays ──────────────── v0.12.4
Installed URIParser ─────────────────── v0.4.1
Installed PDMats ────────────────────── v0.10.1
Installed ArgCheck ──────────────────── v2.1.0
Installed Primes ────────────────────── v0.4.0
Installed TableTraits ───────────────── v1.0.0
Installed Missings ──────────────────── v0.4.4
Installed QuadGK ────────────────────── v2.4.1
Installed Parsers ───────────────────── v1.0.11
Installed SentinelArrays ────────────── v1.2.16
Installed NewickTree ────────────────── v0.2.0
Installed Distributions ─────────────── v0.24.0
Installed OrderedCollections ────────── v1.3.1
Installed MacroTools ────────────────── v0.5.6
Installed DiffResults ───────────────── v1.0.2
Installed LogDensityProblems ────────── v0.10.3
Installed DataFrames ────────────────── v0.21.8
Installed AbstractTrees ─────────────── v0.3.3
Installed TransformVariables ────────── v0.3.10
Installed PooledArrays ──────────────── v0.5.3
Installed BinaryProvider ────────────── v0.5.10
Installed BenchmarkTools ────────────── v0.5.0
Installed SortingAlgorithms ─────────── v0.3.1
Installed NaNMath ───────────────────── v0.3.4
Installed ForwardDiff ───────────────── v0.10.12
Installed Tables ────────────────────── v1.1.0
Installed DocStringExtensions ───────── v0.8.3
Installed DataAPI ───────────────────── v1.3.0
Installed DataStructures ────────────── v0.18.7
Installed StatsFuns ─────────────────── v0.9.5
Installed DataValueInterfaces ───────── v1.0.0
Installed StructTypes ───────────────── v1.1.0
Installed CommonSubexpressions ──────── v0.3.0
Installed DistributedArrays ─────────── v0.6.5
Installed UnPack ────────────────────── v1.0.2
Installed Requires ──────────────────── v1.1.0
Installed Parameters ────────────────── v0.12.1
Installed StatsBase ─────────────────── v0.33.2
Installed CSV ───────────────────────── v0.7.7
Updating /data/cintia/Whale_run/whale_env/Project.toml
[eab5b8f2] + Whale v2.0.1 #master (https://github.com/arzwa/Whale.jl)
Updating /data/cintia/Whale_run/whale_env/Manifest.toml
[1520ce14] + AbstractTrees v0.3.3
[dce04be8] + ArgCheck v2.1.0
[6e4b80f9] + BenchmarkTools v0.5.0
[9e28174c] + BinDeps v1.0.1
[b99e7846] + BinaryProvider v0.5.10
[336ed68f] + CSV v0.7.7
[324d7699] + CategoricalArrays v0.8.3
[bbf7d656] + CommonSubexpressions v0.3.0
[34da2185] + Compat v3.20.0
[9a962f9c] + DataAPI v1.3.0
[a93c6f00] + DataFrames v0.21.8
[864edb3b] + DataStructures v0.18.7
[e2d170a0] + DataValueInterfaces v1.0.0
[163ba53b] + DiffResults v1.0.2
[b552c78f] + DiffRules v1.0.1
[aaf54ef3] + DistributedArrays v0.6.5
[31c24e10] + Distributions v0.24.0
[ffbed154] + DocStringExtensions v0.8.3
[1a297f60] + FillArrays v0.9.7
[f6369f11] + ForwardDiff v0.10.12
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.1
[6fdf6af0] + LogDensityProblems v0.10.3
[1914dd2f] + MacroTools v0.5.6
[e1d29d7a] + Missings v0.4.4
[77ba4419] + NaNMath v0.3.4
[b0a14db8] + NewickTree v0.2.0
[bac558e1] + OrderedCollections v1.3.1
[90014a1f] + PDMats v0.10.1
[d96e819e] + Parameters v0.12.1
[69de0a69] + Parsers v1.0.11
[2dfb63ee] + PooledArrays v0.5.3
[27ebfcd6] + Primes v0.4.0
[1fd47b50] + QuadGK v2.4.1
[189a3867] + Reexport v0.2.0
[ae029012] + Requires v1.1.0
[79098fc4] + Rmath v0.6.0
[91c51154] + SentinelArrays v1.2.16
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.8.0
[90137ffa] + StaticArrays v0.12.4
[2913bbd2] + StatsBase v0.33.2
[4c63d2b9] + StatsFuns v0.9.5
[856f2bd8] + StructTypes v1.1.0
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v1.1.0
[84d833dd] + TransformVariables v0.3.10
[30578b45] + URIParser v0.4.1
[3a884ed6] + UnPack v1.0.2
[eab5b8f2] + Whale v2.0.1 #master (https://github.com/arzwa/Whale.jl)
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Rmath ───────────→ ~/.julia/packages/Rmath/BoBag/deps/build.log
Building SpecialFunctions → ~/.julia/packages/SpecialFunctions/ne2iw/deps/build.log

As you can see, NewickTree should be installed too

So I call the libraries:

julia> using Whale, DynamicHMC, DynamicHMC.Diagnostics, Random, NewickTree, DataFrames
[ Info: Precompiling DynamicHMC [bbc10e6e-7c05-544b-b16e-64fede858acb]
ERROR: ArgumentError: Package NewickTree not found in current path:
- Run ``import Pkg; Pkg.add("NewickTree")`` to install the NewickTree package.
Stacktrace:
[1] require(::Module, ::Symbol) at ./loading.jl:823

I add NewickTree as suggested and it is working so far.

Thank you
Cintia