Is using MCMCBenchmarks
supposed to result in this?
julia> using MCMCBenchmarks
[ Info: Precompiling MCMCBenchmarks [72ce6e51-3f7f-5ebd-8e88-b86aa3e31c30]
using Documenter
β Warning: The call to compilecache failed to create a usable precompiled cache file for Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0]
β exception = Required dependency Rmath [79098fc4-a85e-5d69-aa6a-4863f24498fa] failed to load from a cache file.
β @ Base loading.jl:1025
β Warning: The call to compilecache failed to create a usable precompiled cache file for Bijectors [76274a88-744f-5084-9051-94815aaf08c4]
β exception = Required dependency Tracker [9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c] failed to load from a cache file.
β @ Base loading.jl:1025
Building Libtask β `~/.julia/packages/Libtask/RjRkK/deps/build.log`
Building Libtask β `~/.julia/packages/Libtask/RjRkK/deps/build.log`
β Warning: The call to compilecache failed to create a usable precompiled cache file for Optim [429524aa-4258-5aef-a3af-852621145aeb]
β exception = Required dependency LineSearches [d3d80556-e9d4-5f37-9878-2ab0fcc64255] failed to load from a cache file.
β @ Base loading.jl:1025
β Warning: The call to compilecache failed to create a usable precompiled cache file for KernelDensity [5ab0869b-81aa-558d-bb23-cbf5423bbe9b]
β exception = Invalid input in module list: expected StaticArrays.
β @ Base loading.jl:1025
β Warning: The call to compilecache failed to create a usable precompiled cache file for MCMCChains [c7f686f2-ff18-58e9-bc7b-31028e88f75d]
β exception = Invalid input in module list: expected KernelDensity.
β @ 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 **
β Warning: Replacing module `Optim`
β @ Base loading.jl:931
β Warning: Module Zygote with build ID 1976319913012 is missing from the cache.
β This may mean Zygote [e88e6eb3-aa80-5325-afca-941959d7151f] does not support precompilation but is imported by a module that does.
β @ Base loading.jl:1000
β Warning: Module MCMCChains with build ID 1972946722150 is missing from the cache.
β This may mean MCMCChains [c7f686f2-ff18-58e9-bc7b-31028e88f75d] does not support precompilation but is imported by a module that does.
β @ Base loading.jl:1000
β Warning: The call to compilecache failed to create a usable precompiled cache file for Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0]
β exception = Required dependency Libtask [6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f] failed to load from a cache file.
β @ Base loading.jl:1025
β Warning: Environment variable CMDSTAN_HOME not set. Use set_cmdstan_home!.
β @ CmdStan ~/.julia/packages/CmdStan/NoDBJ/src/CmdStan.jl:27
β Warning: Module Distances with build ID 2070925189279 is missing from the cache.
β This may mean Distances [b4f34e82-e78d-54a5-968a-f98e89d6e8f7] does not support precompilation but is imported by a module that does.
β @ Base loading.jl:1000
β Warning: The call to compilecache failed to create a usable precompiled cache file for Clustering [aaaa29a8-35af-508c-8bc3-b662a17a0fe5]
β exception = Required dependency Distances [b4f34e82-e78d-54a5-968a-f98e89d6e8f7] failed to load from a cache file.
β @ Base loading.jl:1025
β Warning: The call to compilecache failed to create a usable precompiled cache file for StatsPlots [f3b207a7-027a-5e70-b257-86293d7955fd]
β exception = Required dependency Widgets [cc8bc4a8-27d6-5769-a93b-9d913e69aa62] failed to load from a cache file.
β @ Base loading.jl:1025
β Warning: Module Optim with build ID 1956363558772 is missing from the cache.
β This may mean Optim [429524aa-4258-5aef-a3af-852621145aeb] does not support precompilation but is imported by a module that does.
β @ Base loading.jl:1000
β Warning: Module Optim with build ID 1956363558772 is missing from the cache.
β This may mean Optim [429524aa-4258-5aef-a3af-852621145aeb] does not support precompilation but is imported by a module that does.
β @ Base loading.jl:1000
β Warning: Environment variable CMDSTAN_HOME not set. Use set_cmdstan_home!.
β @ CmdStan ~/.julia/packages/CmdStan/NoDBJ/src/CmdStan.jl:27
β Warning: The call to compilecache failed to create a usable precompiled cache file for MCMCBenchmarks [72ce6e51-3f7f-5ebd-8e88-b86aa3e31c30]
β exception = Invalid input in module list: expected Rmath.
β @ 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]
β Warning: Error requiring LogDensityProblems from Turing:
β UndefVarError: AbstractLogDensityProblem not defined
β Stacktrace:
β [1] top-level scope at /home/fredrik/.julia/packages/Turing/fbY6B/src/Turing.jl:144
β [2] eval(::Module, ::Any) at ./boot.jl:330
β [3] top-level scope at /home/fredrik/dev/MCMCBenchmarks/src/MCMCBenchmarks.jl:5
β [4] eval at ./boot.jl:330 [inlined]
β [5] eval at /home/fredrik/.julia/packages/Turing/fbY6B/src/Turing.jl:1 [inlined]
β [6] (::getfield(Turing, Symbol("##7#11")))() at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:67 [0/534]
β [7] err(::getfield(Turing, Symbol("##7#11")), ::Module, ::String) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:38
β [8] #6 at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:66 [inlined]
β [9] withpath(::getfield(Turing, Symbol("##6#10")), ::String) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:28
β [10] #5 at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:65 [inlined]
β [11] listenpkg(::getfield(Turing, Symbol("##5#9")), ::Base.PkgId) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:13
β [12] macro expansion at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:64 [inlined]
β [13] (::getfield(Turing, Symbol("##4#8")))() at /home/fredrik/.julia/packages/Requires/9Jse8/src/init.jl:11
β [14] __init__() at /home/fredrik/.julia/packages/Requires/9Jse8/src/init.jl:18
β [15] _include_from_serialized(::String, ::Array{Any,1}) at ./loading.jl:685
β [16] _require_from_serialized(::String) at ./loading.jl:736
β [17] _require(::Base.PkgId) at ./loading.jl:1023
β [18] require(::Base.PkgId) at ./loading.jl:911
β [19] require(::Module, ::Symbol) at ./loading.jl:906
β [20] include at ./boot.jl:328 [inlined]
β [21] include_relative(::Module, ::String) at ./loading.jl:1094
β [22] _require(::Base.PkgId) at ./loading.jl:1042
β [23] require(::Base.PkgId) at ./loading.jl:911
β [24] require(::Module, ::Symbol) at ./loading.jl:906
β [25] eval(::Module, ::Any) at ./boot.jl:330
β [26] eval_user_input(::Any, ::REPL.REPLBackend) at /home/fredrik/julia12/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:86
β [27] macro expansion at /home/fredrik/julia12/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:118 [inlined]
β [28] (::getfield(REPL, Symbol("##26#27")){REPL.REPLBackend})() at ./task.jl:268
β @ Requires ~/.julia/packages/Requires/9Jse8/src/require.jl:40
[ Info: Precompiling DynamicHMC [bbc10e6e-7c05-544b-b16e-64fede858acb]
β Warning: Module Optim with build ID 1956363558772 is missing from the cache.
β This may mean Optim [429524aa-4258-5aef-a3af-852621145aeb] does not support precompilation but is imported by a module that does.
β @ Base loading.jl:1000
[ Info: Skipping precompilation since __precompile__(false). Importing DynamicHMC [bbc10e6e-7c05-544b-b16e-64fede858acb].
β Warning: Error requiring DynamicHMC from Turing:
β UndefVarError: NUTS_init_tune_mcmc not defined
β Stacktrace:
β [1] top-level scope at /home/fredrik/.julia/packages/Turing/fbY6B/src/Turing.jl:161
β [2] eval(::Module, ::Any) at ./boot.jl:330
β [3] top-level scope at /home/fredrik/dev/MCMCBenchmarks/src/MCMCBenchmarks.jl:6
β [4] eval at ./boot.jl:330 [inlined]
β [5] eval at /home/fredrik/.julia/packages/Turing/fbY6B/src/Turing.jl:1 [inlined]
β [6] (::getfield(Turing, Symbol("##15#19")))() at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:67
β [7] err(::getfield(Turing, Symbol("##15#19")), ::Module, ::String) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:38
β [8] #14 at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:66 [inlined]
β [9] withpath(::getfield(Turing, Symbol("##14#18")), ::String) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:28
β [10] (::getfield(Turing, Symbol("##13#17")))() at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:65
β [11] #invokelatest#1 at ./essentials.jl:790 [inlined]
β [12] invokelatest at ./essentials.jl:789 [inlined]
β [13] #3 at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:19 [inlined]
β [14] iterate at ./generator.jl:47 [inlined]
β [15] _collect(::Array{Function,1}, ::Base.Generator{Array{Function,1},getfield(Requires, Symbol("##3#4"))}, ::Base.EltypeUnknown, ::Base.HasShape{1}) at ./array.jl:619
β [16] map at ./array.jl:548 [inlined]
β [17] loadpkg(::Base.PkgId) at /home/fredrik/.julia/packages/Requires/9Jse8/src/require.jl:19
β [18] #invokelatest#1 at ./essentials.jl:790 [inlined]
β [19] invokelatest at ./essentials.jl:789 [inlined]
β [20] require(::Base.PkgId) at ./loading.jl:914
β [21] require(::Module, ::Symbol) at ./loading.jl:906
β [22] include at ./boot.jl:328 [inlined]
β [23] include_relative(::Module, ::String) at ./loading.jl:1094
β [24] _require(::Base.PkgId) at ./loading.jl:1042
β [25] require(::Base.PkgId) at ./loading.jl:911
β [26] require(::Module, ::Symbol) at ./loading.jl:906
β [27] eval(::Module, ::Any) at ./boot.jl:330
β [28] eval_user_input(::Any, ::REPL.REPLBackend) at /home/fredrik/julia12/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:86
β [29] macro expansion at /home/fredrik/julia12/usr/share/julia/stdlib/v1.2/REPL/src/REPL.jl:118 [inlined]
β [30] (::getfield(REPL, Symbol("##26#27")){REPL.REPLBackend})() at ./task.jl:268
β @ Requires ~/.julia/packages/Requires/9Jse8/src/require.jl:40
I wanted to have a look at the problem but would be good if you could make the package load first.