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TuringLang / Turing.jl

Bayesian inference with probabilistic programming.
https://turinglang.org
MIT License
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Turing compilation fails #1229

Closed astrozot closed 4 years ago

astrozot commented 4 years ago

I have troubles compiling Turing:

julia> using Turing
[ Info: Precompiling Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0]
WARNING: could not import MCMCChains.AbstractChains into Turing
ERROR: LoadError: LoadError: UndefVarError: AbstractChains not defined
Stacktrace:
 [1] include(::Module, ::String) at ./Base.jl:377
 [2] include(::String) at /Users/mlombard/.julia/packages/Turing/xFzfF/src/Turing.jl:1
 [3] top-level scope at /Users/mlombard/.julia/packages/Turing/xFzfF/src/Turing.jl:124
 [4] include(::Module, ::String) at ./Base.jl:377
 [5] top-level scope at none:2
 [6] eval at ./boot.jl:331 [inlined]
 [7] eval(::Expr) at ./client.jl:449
 [8] top-level scope at ./none:3
in expression starting at /Users/mlombard/.julia/packages/Turing/xFzfF/src/utilities/Utilities.jl:6
in expression starting at /Users/mlombard/.julia/packages/Turing/xFzfF/src/Turing.jl:124
ERROR: Failed to precompile Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0] to /Users/mlombard/.julia/compiled/v1.4/Turing/gm4QC_U4o0J.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1272
 [3] _require(::Base.PkgId) at ./loading.jl:1029
 [4] require(::Base.PkgId) at ./loading.jl:927
 [5] require(::Module, ::Symbol) at ./loading.jl:922

Strangely enough if I check the packages I have installed, I do not see MCMCChains:

(@v1.4) pkg> st -m
Status `~/.julia/environments/v1.4/Manifest.toml`
  [621f4979] AbstractFFTs v0.5.0
  [80f14c24] AbstractMCMC v1.0.1
  [85c772de] AbstractNumbers v0.2.1
  [537997a7] AbstractPlotting v0.10.1
  [1520ce14] AbstractTrees v0.3.3
  [79e6a3ab] Adapt v1.0.1
  [0bf59076] AdvancedHMC v0.2.24
  [dce04be8] ArgCheck v2.0.0
  [ec485272] ArnoldiMethod v0.0.4
  [7d9fca2a] Arpack v0.4.0
  [68821587] Arpack_jll v3.5.0+3
  [4fba245c] ArrayInterface v2.8.5
  [4c555306] ArrayLayouts v0.2.4
  [c7932e45] AstroLib v0.4.0
  [c61b5328] AstroTime v0.6.0
  [13072b0f] AxisAlgorithms v1.0.0
  [39de3d68] AxisArrays v0.4.3
  [6e4b80f9] BenchmarkTools v0.5.0
  [76274a88] Bijectors v0.4.0
  [b99e7846] BinaryProvider v0.5.8
  [6e34b625] Bzip2_jll v1.0.6+2
  [fa961155] CEnum v0.2.0
  [3895d2a7] CUDAapi v4.0.0
  [c5f51814] CUDAdrv v6.2.2
  [be33ccc6] CUDAnative v3.0.4
  [49dc2e85] Calculus v0.5.1
  [7057c7e9] Cassette v0.3.3
  [324d7699] CategoricalArrays v0.7.7
  [aaaa29a8] Clustering v0.14.0
  [da1fd8a2] CodeTracking v0.5.9
  [944b1d66] CodecZlib v0.7.0
  [a2cac450] ColorBrewer v0.4.0
  [35d6a980] ColorSchemes v3.8.0
  [3da002f7] ColorTypes v0.9.1
  [c3611d14] ColorVectorSpace v0.8.5
  [5ae59095] Colors v0.11.2
  [861a8166] Combinatorics v1.0.0
  [bbf7d656] CommonSubexpressions v0.2.0
  [34da2185] Compat v2.2.0
  [e66e0078] CompilerSupportLibraries_jll v0.3.3+0
  [a81c6b42] Compose v0.8.2
  [8f4d0f93] Conda v1.4.1
  [88cd18e8] ConsoleProgressMonitor v0.1.2
  [187b0558] ConstructionBase v1.0.0
  [d38c429a] Contour v0.5.2
  [76746363] Cosmology v1.0.0 #master (https://github.com/JuliaAstro/Cosmology.jl)
  [7ad07ef1] CoupledFields v0.2.0
  [a8cc5b0e] Crayons v4.0.1
  [f68482b8] Cthulhu v1.0.2
  [3a865a2d] CuArrays v2.1.0
  [9a962f9c] DataAPI v1.2.0
  [864edb3b] DataStructures v0.17.13
  [e2d170a0] DataValueInterfaces v1.0.0
  [e7dc6d0d] DataValues v0.4.13
  [31a5f54b] Debugger v0.6.4
  [163ba53b] DiffResults v1.0.2
  [b552c78f] DiffRules v1.0.1
  [b4f34e82] Distances v0.8.2
  [aaf54ef3] DistributedArrays v0.6.4
  [31c24e10] Distributions v0.23.2
  [ced4e74d] DistributionsAD v0.1.1
  [ffbed154] DocStringExtensions v0.8.1
  [e30172f5] Documenter v0.24.9
  [732a3c5d] EarthOrientation v0.6.1
  [da5c29d0] EllipsisNotation v0.4.0
  [e2ba6199] ExprTools v0.1.1
  [c87230d0] FFMPEG v0.3.0
  [b22a6f82] FFMPEG_jll v4.1.0+2
  [7a1cc6ca] FFTW v1.1.0
  [525bcba6] FITSIO v0.14.0
  [5789e2e9] FileIO v1.2.4
  [1a297f60] FillArrays v0.8.7
  [6a86dc24] FiniteDiff v2.3.0
  [26cc04aa] FiniteDifferences v0.9.6
  [53c48c17] FixedPointNumbers v0.7.1
  [587475ba] Flux v0.10.4
  [59287772] Formatting v0.4.1
  [f6369f11] ForwardDiff v0.10.10
  [b38be410] FreeType v3.0.0
  [d7e528f0] FreeType2_jll v2.10.1+2
  [663a7486] FreeTypeAbstraction v0.7.0
  [559328eb] FriBidi_jll v1.0.5+2
  [f7f18e0c] GLFW v3.2.2
  [0656b61e] GLFW_jll v3.3.2+0
  [38e38edf] GLM v1.3.9
  [e9467ef8] GLMakie v0.1.0
  [0c68f7d7] GPUArrays v3.2.0
  [28b8d3ca] GR v0.48.0
  [c91e804a] Gadfly v1.0.1
  [5c1252a2] GeometryBasics v0.2.4
  [4d00f742] GeometryTypes v0.8.2
  [a2bd30eb] Graphics v1.0.2
  [cd3eb016] HTTP v0.8.14
  [a1b4810d] Hexagons v0.2.0
  [eafb193a] Highlights v0.4.5
  [7073ff75] IJulia v1.21.2
  [7869d1d1] IRTools v0.3.2
  [a09fc81d] ImageCore v0.8.14
  [6218d12a] ImageMagick v1.1.4
  [c73af94c] ImageMagick_jll v6.9.10-12+1
  [9b13fd28] IndirectArrays v0.5.1
  [d25df0c9] Inflate v0.1.2
  [83e8ac13] IniFile v0.5.0
  [505f98c9] InplaceOps v0.3.0
  [1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
  [c8ce9da6] IntelVectorMath v0.4.0
  [a98d9a8b] Interpolations v0.12.9
  [8197267c] IntervalSets v0.4.0
  [d5eda45b] ItemGraphs v0.4.0
  [c8e1da08] IterTools v1.3.0
  [82899510] IteratorInterfaceExtensions v1.0.0
  [682c06a0] JSON v0.21.0
  [aacddb02] JpegTurbo_jll v2.0.1+0
  [aa1ae85d] JuliaInterpreter v0.7.13
  [e5e0dc1b] Juno v0.8.1
  [5ab0869b] KernelDensity v0.5.1
  [c1c5ebd0] LAME_jll v3.100.0+0
  [929cbde3] LLVM v1.3.4
  [2f5f767c] LeapSeconds v1.1.0
  [1d6d02ad] LeftChildRightSiblingTrees v0.1.2
  [dd192d2f] LibVPX_jll v1.8.1+1
  [d4300ac3] Libgcrypt_jll v1.8.5+1
  [7e76a0d4] Libglvnd_jll v1.3.0+1
  [7add5ba3] Libgpg_error_jll v1.36.0+1
  [94ce4f54] Libiconv_jll v1.16.0+2
  [6f1fad26] Libtask v0.3.4
  [89763e89] Libtiff_jll v4.0.10+1
  [093fc24a] LightGraphs v1.3.1
  [d3d80556] LineSearches v7.0.1
  [4345ca2d] Loess v0.5.1
  [e6f89c97] LoggingExtras v0.4.0
  [6f1432cf] LoweredCodeUtils v0.4.3
  [c7f686f2] MCMCChains v3.0.12
  [33e6dc65] MKL v0.2.0 #master (https://github.com/JuliaComputing/MKL.jl.git)
  [856f044c] MKL_jll v2020.0.166+0
  [1914dd2f] MacroTools v0.5.5
  [ee78f7c6] Makie v0.10.0
  [dbb5928d] MappedArrays v0.2.2
  [739be429] MbedTLS v1.0.2
  [c8ffd9c3] MbedTLS_jll v2.16.0+2
  [eff96d63] Measurements v2.1.1
  [442fdcdd] Measures v0.3.1
  [e89f7d12] Media v0.5.0
  [7269a6da] MeshIO v0.4.0
  [e1d29d7a] Missings v0.4.3
  [66fc600b] ModernGL v1.1.2
  [e94cdb99] MosaicViews v0.2.2
  [46d2c3a1] MuladdMacro v0.2.2
  [6f286f6a] MultivariateStats v0.7.0
  [d41bc354] NLSolversBase v7.6.1
  [2774e3e8] NLsolve v4.3.0
  [872c559c] NNlib v0.6.6
  [77ba4419] NaNMath v0.3.3
  [b8a86587] NearestNeighbors v0.4.4
  [510215fc] Observables v0.3.1
  [6fe1bfb0] OffsetArrays v1.0.4
  [e7412a2a] Ogg_jll v1.3.3+0
  [4536629a] OpenBLAS_jll v0.3.9+2
  [458c3c95] OpenSSL_jll v1.1.1+2
  [efe28fd5] OpenSpecFun_jll v0.5.3+3
  [429524aa] Optim v0.20.1
  [fbd9d27c] OptionalData v0.3.0
  [91d4177d] Opus_jll v1.3.1+0
  [bac558e1] OrderedCollections v1.1.0
  [90014a1f] PDMats v0.9.12
  [9b87118b] PackageCompiler v1.1.1
  [19eb6ba3] Packing v0.4.0
  [5432bcbf] PaddedViews v0.5.5
  [d96e819e] Parameters v0.12.0
  [69de0a69] Parsers v0.3.12
  [ccf2f8ad] PlotThemes v1.0.3
  [995b91a9] PlotUtils v0.6.5
  [91a5bcdd] Plots v1.0.13
  [f27b6e38] Polynomials v0.5.3
  [85a6dd25] PositiveFactorizations v0.2.3
  [27ebfcd6] Primes v0.4.0
  [49802e3a] ProgressBars v0.7.1
  [33c8b6b6] ProgressLogging v0.1.2
  [92933f4c] ProgressMeter v1.2.0
  [1fd47b50] QuadGK v2.3.1
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.4.0
  [3cdcf5f2] RecipesBase v1.0.0
  [01d81517] RecipesPipeline v0.1.4
  [189a3867] Reexport v0.2.0
  [cbe49d4c] RemoteFiles v0.3.1
  [ae029012] Requires v0.5.2
  [295af30f] Revise v2.6.1
  [79098fc4] Rmath v0.6.1
  [f50d1b31] Rmath_jll v0.2.2+0
  [f2b01f46] Roots v1.0.1
  [65257c39] ShaderAbstractions v0.2.1
  [1277b4bf] ShiftedArrays v1.0.0
  [992d4aef] Showoff v0.3.1
  [73760f76] SignedDistanceFields v0.4.0
  [699a6c99] SimpleTraits v0.9.2
  [b85f4697] SoftGlobalScope v1.0.10
  [a2af1166] SortingAlgorithms v0.3.1
  [276daf66] SpecialFunctions v0.10.0
  [90137ffa] StaticArrays v0.12.1
  [2913bbd2] StatsBase v0.32.2
  [4c63d2b9] StatsFuns v0.9.4
  [65254759] StatsMakie v0.2.1
  [3eaba693] StatsModels v0.6.11
  [f3b207a7] StatsPlots v0.14.5
  [09ab397b] StructArrays v0.4.3
  [ab02a1b2] TableOperations v0.2.1
  [3783bdb8] TableTraits v1.0.0
  [bd369af6] Tables v1.0.4
  [d3a6a179] TerminalExtensions v0.4.0
  [5d786b92] TerminalLoggers v0.1.1
  [a759f4b9] TimerOutputs v0.5.4
  [37b6cedf] Traceur v0.3.0
  [9f7883ad] Tracker v0.2.6
  [3bb67fe8] TranscodingStreams v0.9.5
  [fce5fe82] Turing v0.7.1
  [1cfade01] UnicodeFun v0.4.1
  [1986cc42] Unitful v1.1.0
  [6fb2a4bd] UnitfulAngles v0.6.1
  [6112ee07] UnitfulAstro v1.0.1
  [81def892] VersionParsing v1.2.0
  [cc8bc4a8] Widgets v0.6.2
  [efce3f68] WoodburyMatrices v0.5.2
  [02c8fc9c] XML2_jll v2.9.9+4
  [aed1982a] XSLT_jll v1.1.33+2
  [cf2f014d] Xorg_fixesproto_jll v5.0.0+0
  [84d6cd60] Xorg_inputproto_jll v2.3.2+1
  [4f6342f7] Xorg_libX11_jll v1.6.9+2
  [0c0b7dd1] Xorg_libXau_jll v1.0.9+2
  [935fb764] Xorg_libXcursor_jll v1.2.0+2
  [a3789734] Xorg_libXdmcp_jll v1.1.3+2
  [1082639a] Xorg_libXext_jll v1.3.4+2
  [d091e8ba] Xorg_libXfixes_jll v5.0.3+2
  [a51aa0fd] Xorg_libXi_jll v1.7.10+2
  [d1454406] Xorg_libXinerama_jll v1.1.4+2
  [ec84b674] Xorg_libXrandr_jll v1.5.2+2
  [ea2f1a96] Xorg_libXrender_jll v0.9.10+2
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.0+1
  [c7cfdc94] Xorg_libxcb_jll v1.13.0+2
  [0e394dc1] Xorg_randrproto_jll v1.5.0+0
  [21e99dc2] Xorg_renderproto_jll v0.11.1+1
  [7c09cfe3] Xorg_util_macros_jll v1.19.2+1
  [c2e9c405] Xorg_xcb_proto_jll v1.13.0+1
  [d13bc2ba] Xorg_xextproto_jll v7.3.0+1
  [6a3da44c] Xorg_xineramaproto_jll v1.2.1+0
  [46797783] Xorg_xproto_jll v7.0.31+1
  [c5fb5394] Xorg_xtrans_jll v1.4.0+1
  [c2297ded] ZMQ v1.2.0
  [8f1865be] ZeroMQ_jll v4.3.2+2
  [a5390f91] ZipFile v0.9.1
  [83775a58] Zlib_jll v1.2.11+9
  [3161d3a3] Zstd_jll v1.4.4+0
  [e88e6eb3] Zygote v0.4.15
  [700de1a5] ZygoteRules v0.2.0
  [0ac62f75] libass_jll v0.14.0+1
  [f638f0a6] libfdk_aac_jll v0.1.6+1
  [b53b4c65] libpng_jll v1.6.37+3
  [f27f6e37] libvorbis_jll v1.3.6+2
  [1270edf5] x264_jll v2019.5.25+1
  [dfaa095f] x265_jll v3.0.0+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

I tried to update the packages and also to install MCMCChains, but with no luck.

cpfiffer commented 4 years ago

Your version of Turing is out of date and one of the other packages you have is preventing it from updating to the current version of 0.11.0.

Please see any of these issues or the Discouse post:

astrozot commented 4 years ago

Thank you so much! For reference, it was Gadfly...