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arzwa / Whale.jl

Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation
GNU Lesser General Public License v2.1
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Error to install Whale #2

Open cintiaiha opened 4 years ago

cintiaiha commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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