Unable to load MCMCBenchmarks

[itsdfish]

A user reported that MCMCBenchmarks does not load on his linux system. Unfortunately, I am not able to reproduce the problem on my system or Travis.

Sometimes I encounter a compilecache failure when something in my environment changes after adding or updating packages. Revise might be implicated in the issue but I'm not sure. In either case, these errors have never prevented MCMCBenchmarks from loading for me.

Rob, have you experienced this type of problem?

Error/warning

julia> using MCMCBenchmarks
[ Info: Precompiling MCMCBenchmarks [72ce6e51-3f7f-5ebd-8e88-b86aa3e31c30]
using Documenter
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0]
│   exception = Required dependency Rmath [79098fc4-a85e-5d69-aa6a-4863f24498fa] failed to load from a cache file.
└ @ Base loading.jl:1025
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Bijectors [76274a88-744f-5084-9051-94815aaf08c4]
│   exception = Required dependency Tracker [9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c] failed to load from a cache file.
└ @ Base loading.jl:1025
  Building Libtask → `~/.julia/packages/Libtask/RjRkK/deps/build.log`
  Building Libtask → `~/.julia/packages/Libtask/RjRkK/deps/build.log`
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Optim [429524aa-4258-5aef-a3af-852621145aeb]
│   exception = Required dependency LineSearches [d3d80556-e9d4-5f37-9878-2ab0fcc64255] failed to load from a cache file.
└ @ Base loading.jl:1025
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for KernelDensity [5ab0869b-81aa-558d-bb23-cbf5423bbe9b]
│   exception = Invalid input in module list: expected StaticArrays.
└ @ Base loading.jl:1025
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for MCMCChains [c7f686f2-ff18-58e9-bc7b-31028e88f75d]
│   exception = Invalid input in module list: expected KernelDensity.
└ @ Base loading.jl:1025
WARNING: Method definition dot(Array{T, N} where N where T, LinearAlgebra.Diagonal{T, V} where V<:AbstractArray{T, 1} where T, Array{T, N} where N where T) in module Optim at /home/fredrik/.julia/packages/Optim/
tAcSy/src/multivariate/precon.jl:46 overwritten in module Optim at /home/fredrik/.julia/packages/Optim/tAcSy/src/multivariate/precon.jl:46.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition dot(Any, Nothing, Any) in module Optim at /home/fredrik/.julia/packages/Optim/tAcSy/src/multivariate/precon.jl:36 overwritten in module Optim at /home/fredrik/.julia/packages/Optim/tAc
Sy/src/multivariate/precon.jl:36.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition dot(Any, Any, Any) in module Optim at /home/fredrik/.julia/packages/Optim/tAcSy/src/multivariate/precon.jl:23 overwritten in module Optim at /home/fredrik/.julia/packages/Optim/tAcSy/s
rc/multivariate/precon.jl:23.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition ldiv!(Array{T, N} where N where T, LinearAlgebra.Diagonal{T, V} where V<:AbstractArray{T, 1} where T, Array{T, N} where N where T) in module Optim at /home/fredrik/.julia/packages/Opti
m/tAcSy/src/multivariate/precon.jl:45 overwritten in module Optim at /home/fredrik/.julia/packages/Optim/tAcSy/src/multivariate/precon.jl:45.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition ldiv!(Any, Nothing, Any) in module Optim at /home/fredrik/.julia/packages/Optim/tAcSy/src/multivariate/precon.jl:34 overwritten in module Optim at /home/fredrik/.julia/packages/Optim/t
AcSy/src/multivariate/precon.jl:34.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition ldiv!(Any, AbstractArray{T, 2} where T, Any) in module Optim at /home/fredrik/.julia/packages/Optim/tAcSy/src/multivariate/precon.jl:64 overwritten in module Optim at /home/fredrik/.ju
lia/packages/Optim/tAcSy/src/multivariate/precon.jl:64.
  ** incremental compilation may be fatally broken for this module **

┌ Warning: Replacing module `Optim`
└ @ Base loading.jl:931
┌ Warning: Module Zygote with build ID 1976319913012 is missing from the cache.
│ This may mean Zygote [e88e6eb3-aa80-5325-afca-941959d7151f] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1000
┌ Warning: Module MCMCChains with build ID 1972946722150 is missing from the cache.
│ This may mean MCMCChains [c7f686f2-ff18-58e9-bc7b-31028e88f75d] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1000
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0]
│   exception = Required dependency Libtask [6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f] failed to load from a cache file.
└ @ Base loading.jl:1025
┌ Warning: Environment variable CMDSTAN_HOME not set. Use set_cmdstan_home!.
└ @ CmdStan ~/.julia/packages/CmdStan/NoDBJ/src/CmdStan.jl:27
┌ Warning: Module Distances with build ID 2070925189279 is missing from the cache.
│ This may mean Distances [b4f34e82-e78d-54a5-968a-f98e89d6e8f7] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1000
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Clustering [aaaa29a8-35af-508c-8bc3-b662a17a0fe5]
│   exception = Required dependency Distances [b4f34e82-e78d-54a5-968a-f98e89d6e8f7] failed to load from a cache file.
└ @ Base loading.jl:1025
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for StatsPlots [f3b207a7-027a-5e70-b257-86293d7955fd]
│   exception = Required dependency Widgets [cc8bc4a8-27d6-5769-a93b-9d913e69aa62] failed to load from a cache file.
└ @ Base loading.jl:1025
┌ Warning: Module Optim with build ID 1956363558772 is missing from the cache.
│ This may mean Optim [429524aa-4258-5aef-a3af-852621145aeb] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1000
┌ Warning: Module Optim with build ID 1956363558772 is missing from the cache.
│ This may mean Optim [429524aa-4258-5aef-a3af-852621145aeb] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1000
┌ Warning: Environment variable CMDSTAN_HOME not set. Use set_cmdstan_home!.
└ @ CmdStan ~/.julia/packages/CmdStan/NoDBJ/src/CmdStan.jl:27
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for MCMCBenchmarks [72ce6e51-3f7f-5ebd-8e88-b86aa3e31c30]
│   exception = Invalid input in module list: expected Rmath.
└ @ Base loading.jl:1025
[ Info: Recompiling stale cache file /home/fredrik/.julia/compiled/v1.2/Turing/gm4QC.ji for Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0]
┌ Warning: Error requiring LogDensityProblems from Turing:
│ UndefVarError: AbstractLogDensityProblem not defined
│ Stacktrace:
│  [1] top-level scope at /home/fredrik/.julia/packages/Turing/fbY6B/src/Turing.jl:144
│  [2] eval(::Module, ::Any) at ./boot.jl:330
│  [3] top-level scope at /home/fredrik/dev/MCMCBenchmarks/src/MCMCBenchmarks.jl:5
│  [4] eval at ./boot.jl:330 [inlined]
│  [5] eval at /home/fredrik/.julia/packages/Turing/fbY6B/src/Turing.jl:1 [inlined]
│  [6] (::getfield(Turing, Symbol("##7#11")))() at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:67                                                                                           [0/534]
│  [7] err(::getfield(Turing, Symbol("##7#11")), ::Module, ::String) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:38
│  [8] #6 at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:66 [inlined]
│  [9] withpath(::getfield(Turing, Symbol("##6#10")), ::String) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:28
│  [10] #5 at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:65 [inlined]
│  [11] listenpkg(::getfield(Turing, Symbol("##5#9")), ::Base.PkgId) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:13
│  [12] macro expansion at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:64 [inlined]
│  [13] (::getfield(Turing, Symbol("##4#8")))() at /home/fredrik/.julia/packages/Requires/9Jse8/src/init.jl:11
│  [14] __init__() at /home/fredrik/.julia/packages/Requires/9Jse8/src/init.jl:18
│  [15] _include_from_serialized(::String, ::Array{Any,1}) at ./loading.jl:685
│  [16] _require_from_serialized(::String) at ./loading.jl:736
│  [17] _require(::Base.PkgId) at ./loading.jl:1023
│  [18] require(::Base.PkgId) at ./loading.jl:911
│  [19] require(::Module, ::Symbol) at ./loading.jl:906
│  [20] include at ./boot.jl:328 [inlined]
│  [21] include_relative(::Module, ::String) at ./loading.jl:1094
│  [22] _require(::Base.PkgId) at ./loading.jl:1042
│  [23] require(::Base.PkgId) at ./loading.jl:911
│  [24] require(::Module, ::Symbol) at ./loading.jl:906
│  [25] eval(::Module, ::Any) at ./boot.jl:330
│  [26] eval_user_input(::Any, ::REPL.REPLBackend) at /home/fredrik/julia12/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:86
│  [27] macro expansion at /home/fredrik/julia12/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:118 [inlined]
│  [28] (::getfield(REPL, Symbol("##26#27")){REPL.REPLBackend})() at ./task.jl:268
└ @ Requires ~/.julia/packages/Requires/9Jse8/src/require.jl:40
[ Info: Precompiling DynamicHMC [bbc10e6e-7c05-544b-b16e-64fede858acb]
┌ Warning: Module Optim with build ID 1956363558772 is missing from the cache.
│ This may mean Optim [429524aa-4258-5aef-a3af-852621145aeb] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1000
[ Info: Skipping precompilation since __precompile__(false). Importing DynamicHMC [bbc10e6e-7c05-544b-b16e-64fede858acb].
┌ Warning: Error requiring DynamicHMC from Turing:
│ UndefVarError: NUTS_init_tune_mcmc not defined
│ Stacktrace:
│  [1] top-level scope at /home/fredrik/.julia/packages/Turing/fbY6B/src/Turing.jl:161
│  [2] eval(::Module, ::Any) at ./boot.jl:330
│  [3] top-level scope at /home/fredrik/dev/MCMCBenchmarks/src/MCMCBenchmarks.jl:6
│  [4] eval at ./boot.jl:330 [inlined]
│  [5] eval at /home/fredrik/.julia/packages/Turing/fbY6B/src/Turing.jl:1 [inlined]
│  [6] (::getfield(Turing, Symbol("##15#19")))() at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:67
│  [7] err(::getfield(Turing, Symbol("##15#19")), ::Module, ::String) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:38
│  [8] #14 at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:66 [inlined]
│  [9] withpath(::getfield(Turing, Symbol("##14#18")), ::String) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:28
│  [10] (::getfield(Turing, Symbol("##13#17")))() at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:65
│  [11] #invokelatest#1 at ./essentials.jl:790 [inlined]
│  [12] invokelatest at ./essentials.jl:789 [inlined]
│  [13] #3 at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:19 [inlined]
│  [14] iterate at ./generator.jl:47 [inlined]
│  [15] _collect(::Array{Function,1}, ::Base.Generator{Array{Function,1},getfield(Requires, Symbol("##3#4"))}, ::Base.EltypeUnknown, ::Base.HasShape{1}) at ./array.jl:619
│  [16] map at ./array.jl:548 [inlined]
│  [17] loadpkg(::Base.PkgId) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:19
│  [18] #invokelatest#1 at ./essentials.jl:790 [inlined]
│  [19] invokelatest at ./essentials.jl:789 [inlined]
│  [20] require(::Base.PkgId) at ./loading.jl:914
│  [21] require(::Module, ::Symbol) at ./loading.jl:906
│  [22] include at ./boot.jl:328 [inlined]
│  [23] include_relative(::Module, ::String) at ./loading.jl:1094
│  [24] _require(::Base.PkgId) at ./loading.jl:1042
│  [25] require(::Base.PkgId) at ./loading.jl:911
│  [26] require(::Module, ::Symbol) at ./loading.jl:906
│  [27] eval(::Module, ::Any) at ./boot.jl:330
│  [28] eval_user_input(::Any, ::REPL.REPLBackend) at /home/fredrik/julia12/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:86
│  [29] macro expansion at /home/fredrik/julia12/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:118 [inlined]
│  [30] (::getfield(REPL, Symbol("##26#27")){REPL.REPLBackend})() at ./task.jl:268
└ @ Requires ~/.julia/packages/Requires/9Jse8/src/require.jl:40
```

**Version**

Julia 1.2

```
Project MCMCBenchmarks v0.5.3
    Status `~/dev/MCMCBenchmarks/Manifest.toml`
  [621f4979] AbstractFFTs v0.4.1
  [79e6a3ab] Adapt v1.0.0
  [0bf59076] AdvancedHMC v0.2.5
  [dce04be8] ArgCheck v1.0.1
  [7d9fca2a] Arpack v0.3.1
  [4fba245c] ArrayInterface v1.2.1
  [13072b0f] AxisAlgorithms v1.0.0
  [39de3d68] AxisArrays v0.3.3
  [6e4b80f9] BenchmarkTools v0.4.3
  [76274a88] Bijectors v0.4.0
  [9e28174c] BinDeps v0.8.10
  [b99e7846] BinaryProvider v0.5.6
  [00ebfdb7] CSTParser v0.6.2
  [336ed68f] CSV v0.5.13
  [49dc2e85] Calculus v0.5.0
  [324d7699] CategoricalArrays v0.7.1
  [aaaa29a8] Clustering v0.13.3
  [593b3428] CmdStan v5.2.0
  [da1fd8a2] CodeTracking v0.5.8
  [3da002f7] ColorTypes v0.8.0
  [5ae59095] Colors v0.9.6
  [861a8166] Combinatorics v0.7.0
  [bbf7d656] CommonSubexpressions v0.2.0
  [34da2185] Compat v2.1.0
  [8f4d0f93] Conda v1.3.0
  [d38c429a] Contour v0.5.1
  [a8cc5b0e] Crayons v4.0.0
  [9a962f9c] DataAPI v1.1.0
  [a93c6f00] DataFrames v0.19.4
  [864edb3b] DataStructures v0.17.2
  [e2d170a0] DataValueInterfaces v1.0.0
  [e7dc6d0d] DataValues v0.4.12
  [01453d9d] DiffEqDiffTools v1.3.0
  [163ba53b] DiffResults v0.0.4
  [b552c78f] DiffRules v0.0.10
  [b4f34e82] Distances v0.8.2
  [31c24e10] Distributions v0.21.3
  [ced4e74d] DistributionsAD v0.1.0
  [ffbed154] DocStringExtensions v0.8.1
  [e30172f5] Documenter v0.23.3
  [bbc10e6e] DynamicHMC v2.1.0
  [c87230d0] FFMPEG v0.2.3
  [7a1cc6ca] FFTW v0.3.0
  [1a297f60] FillArrays v0.7.2
  [26cc04aa] FiniteDifferences v0.8.0
  [53c48c17] FixedPointNumbers v0.6.1
  [f6369f11] ForwardDiff v0.10.3
  [28b8d3ca] GR v0.41.0
  [4d00f742] GeometryTypes v0.7.6
  [d9be37ee] Homebrew v0.7.1
  [7869d1d1] IRTools v0.2.3
  [505f98c9] InplaceOps v0.3.0
  [a98d9a8b] Interpolations v0.12.2
  [8197267c] IntervalSets v0.3.2
  [41ab1584] InvertedIndices v1.0.0
  [c8e1da08] IterTools v1.2.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [682c06a0] JSON v0.21.0
  [aa1ae85d] JuliaInterpreter v0.7.4
  [5ab0869b] KernelDensity v0.5.1
  [5078a376] LazyArrays v0.12.2
  [6f1fad26] Libtask v0.3.1
  [d3d80556] LineSearches v7.0.1
  [6fdf6af0] LogDensityProblems v0.9.1
  [6f1432cf] LoweredCodeUtils v0.3.8
  [c7f686f2] MCMCChains v0.3.14
  [6e857e4b] MCMCDiagnostics v0.3.0
  [1914dd2f] MacroTools v0.5.1
  [dbb5928d] MappedArrays v0.2.2
  [442fdcdd] Measures v0.3.0
  [e1d29d7a] Missings v0.4.3
  [d41bc354] NLSolversBase v7.5.0
  [872c559c] NNlib v0.6.0
  [77ba4419] NaNMath v0.3.2
  [86f7a689] NamedArrays v0.9.3
  [b8a86587] NearestNeighbors v0.4.3
  [510215fc] Observables v0.2.3
  [6fe1bfb0] OffsetArrays v0.11.1
  [429524aa] Optim v0.19.3
  [bac558e1] OrderedCollections v1.1.0
  [90014a1f] PDMats v0.9.10
  [d96e819e] Parameters v0.12.0
  [69de0a69] Parsers v0.3.7
  [ccf2f8ad] PlotThemes v0.3.0
  [995b91a9] PlotUtils v0.6.0
  [91a5bcdd] Plots v0.27.0
  [f27b6e38] Polynomials v0.5.2
  [2dfb63ee] PooledArrays v0.5.2
  [85a6dd25] PositiveFactorizations v0.2.2
  [92933f4c] ProgressMeter v1.1.0
  [1fd47b50] QuadGK v2.0.3
  [b3c3ace0] RangeArrays v0.3.1
  [c84ed2f1] Ratios v0.3.1
  [3cdcf5f2] RecipesBase v0.7.0
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v0.5.2
  [295af30f] Revise v2.2.0
  [79098fc4] Rmath v0.5.0
  [f2b01f46] Roots v0.8.3
  [992d4aef] Showoff v0.3.1
  [a2af1166] SortingAlgorithms v0.3.1
  [276daf66] SpecialFunctions v0.7.2
  [90137ffa] StaticArrays v0.11.0
  [2913bbd2] StatsBase v0.32.0
  [4c63d2b9] StatsFuns v0.8.0
  [f3b207a7] StatsPlots v0.12.0
  [3783bdb8] TableTraits v1.0.0
  [bd369af6] Tables v0.2.11
  [a759f4b9] TimerOutputs v0.5.0
  [0796e94c] Tokenize v0.5.6
  [9f7883ad] Tracker v0.2.3
  [84d833dd] TransformVariables v0.3.8
  [fce5fe82] Turing v0.7.0
  [30578b45] URIParser v0.4.0
  [81def892] VersionParsing v1.1.3
  [ea10d353] WeakRefStrings v0.6.1
  [cc8bc4a8] Widgets v0.6.2
  [efce3f68] WoodburyMatrices v0.4.1
  [e88e6eb3] Zygote v0.3.4
  [700de1a5] ZygoteRules v0.1.0
  [2a0f44e3] Base64 
  [ade2ca70] Dates 
  [8bb1440f] DelimitedFiles 
  [8ba89e20] Distributed 
  [7b1f6079] FileWatching 
  [9fa8497b] Future 
  [b77e0a4c] InteractiveUtils 
  [76f85450] LibGit2 
  [8f399da3] Libdl 
  [37e2e46d] LinearAlgebra 
  [56ddb016] Logging 
  [d6f4376e] Markdown 
  [a63ad114] Mmap 
  [44cfe95a] Pkg 
  [de0858da] Printf 
  [9abbd945] Profile 
  [3fa0cd96] REPL 
  [9a3f8284] Random 
  [ea8e919c] SHA 
  [9e88b42a] Serialization 
  [1a1011a3] SharedArrays 
  [6462fe0b] Sockets 
  [2f01184e] SparseArrays 
  [10745b16] Statistics 
  [4607b0f0] SuiteSparse 
  [8dfed614] Test 
  [cf7118a7] UUIDs 
  [4ec0a83e] Unicode
```

[goedman]

Hi Chris, Some of the warnings I see often, e.g. the dot() related messages. Later on it seems issues with versions related to interactions between Turing and DynamicHMC. Not sure I have seen exactly these though. Usually, like you I guess, I make sure I have the latest versions installed and precompiled.

[itsdfish]

I also see warning message from Turing, but I never encountered a situation where they prevented the package from loading. I'm assuming that the package has been loading for you.

[itsdfish]

I was never able to reproduce this error. So I will close this issue.