Turing build error: could not import MCMCChains.AbstractChains into Turing

[uozden]

First of all, best wishes for safety and wellbeing.

[ 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 C:\Users\.....\.julia\packages\Turing\xFzfF\src\Turing.jl:1
 [3] top-level scope at C:\Users\....\.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 C:\Users\-...\.julia\packages\Turing\xFzfF\src\utilities\Utilities.jl:6
in expression starting at C:\Users\...\.julia\packages\Turing\xFzfF\src\Turing.jl:124
ERROR: Failed to precompile Turing [fce5fe82-541a-59a6-adf8-730c64b5f9a0] to C:\Users\........\.julia\compiled\v1.4\Turing\gm4QC_xLDiA.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
``
My system and Environment;
 
`` julia> versioninfo()
Julia Version 1.4.0
Commit b8e9a9ecc6 (2020-03-21 16:36 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
Environment:
  JULIA_MATHKERNEL = C:\Program Files\Wolfram Research\Wolfram Engine\12.0\MathKernel.exe
  JULIA_MATHLINK = C:\Program Files\Wolfram Research\Wolfram Engine\12.0\SystemFiles\Activation\Windows-x86-64\ml64i4.dll ``

[cpfiffer]

A package in your environment is prohibiting you from using the most recent version of Turing, 0.10.1. Try typing ] add Turing@0.10.1 to see which packages are doing this.

[uozden]

@cpfiffer Thank you for your reply. Here is the outcome;

(@v1.4) pkg> add Turing@0.10.1
Resolving package versions... ERROR: Unsatisfiable requirements detected for package Bijectors [76274a88]: Bijectors [76274a88] log: ├─possible versions are: [0.1.0, 0.2.0, 0.2.5-0.2.9, 0.3.0-0.3.2, 0.4.0, 0.5.0-0.5.2, 0.6.0-0.6.6] or uninstalled ├─restricted by compatibility requirements with Turing [fce5fe82] to versions: 0.6.4-0.6.6 │ └─Turing [fce5fe82] log: │ ├─possible versions are: [0.5.0-0.5.1, 0.6.0-0.6.2, 0.6.4-0.6.9, 0.6.11-0.6.15, 0.6.17-0.6.19, 0.6.21-0.6.23, 0.7.0-0.7.4, 0.8.0-0.8.3, 0.9.0-0.9.2, 0.10.0-0.10.1] or uninstalled │ └─restricted to versions 0.10.1 by an explicit requirement, leaving only versions 0.10.1 └─restricted by compatibility requirements with Compat [34da2185] to versions: [0.1.0, 0.2.0, 0.2.5-0.2.9, 0.3.0-0.3.2, 0.4.0, 0.5.0-0.5.2] or uninstalled — no versions left └─Compat [34da2185] log: ├─possible versions are: [1.0.0-1.0.1, 1.1.0, 1.2.0, 1.3.0, 1.4.0, 1.5.0-1.5.1, 2.0.0, 2.1.0, 2.2.0, 3.0.0, 3.1.0, 3.2.0, 3.3.0-3.3.1, 3.4.0, 3.5.0, 3.6.0, 3.7.0, 3.8.0] or uninstalled ├─restricted by compatibility requirements with LIBSVM [b1bec4e5] to versions: [1.0.0-1.0.1, 1.1.0, 1.2.0, 1.3.0, 1.4.0, 1.5.0-1.5.1, 2.0.0, 2.1.0, 2.2.0, 3.0.0, 3.1.0, 3.2.0, 3.3.0-3.3.1, 3.4.0, 3.5.0, 3.6.0, 3.7.0, 3.8.0] │ └─LIBSVM [b1bec4e5] log: │ ├─possible versions are: [0.2.0, 0.3.0-0.3.1, 0.4.0] or uninstalled │ └─restricted to versions * by an explicit requirement, leaving only versions [0.2.0, 0.3.0-0.3.1, 0.4.0] └─restricted by compatibility requirements with Suppressor [fd094767] to versions: [1.0.0-1.0.1, 1.1.0, 1.2.0, 1.3.0, 1.4.0, 1.5.0-1.5.1, 2.0.0, 2.1.0, 2.2.0] └─Suppressor [fd094767] log: ├─possible versions are: 0.1.1 or uninstalled └─restricted to versions * by SpineInterface [0cda1612], leaving only versions 0.1.1 └─SpineInterface [0cda1612] log: ├─possible versions are: 0.1.0 or uninstalled └─SpineInterface [0cda1612] is fixed to version 0.1.0

[cpfiffer]

That is incredibly difficult to read without the original formatting. Put your code in three backticks, like this:

```
here is some code
    that maintains all the spacing
```

Things you can do while you fix the formatting:

1. Remove all your packages and start from a fresh environment, by deleting everything in "C:\Users\your_username\.julia\environments\v1.4\" and then running Julia and calling ] add Turing first.
2. You can use a local environment by activating the directory you are in with ] activate . and then ] add Turing.
3. Try updating everything first with ] update.
4. Manually go through the list of packages that are blocking your update (listed when you call ] add Turing@0.10.1) and remove them.

In any case you can validate your package version with ] status. If you do not see 0.10.1, you are not in the right spot yet.

[uozden]

@cpfiffer Thank you for your response. Here it is;

Updating registry at `C:\Users\....\.julia\registries\General`
   Updating git-repo `https://github.com/JuliaRegistries/General.git`
  Resolving package versions...
ERROR: Unsatisfiable requirements detected for package Bijectors [76274a88]:
 Bijectors [76274a88] log:
 ├─possible versions are: [0.1.0, 0.2.0, 0.2.5-0.2.9, 0.3.0-0.3.2, 0.4.0, 0.5.0-0.5.2, 0.6.0-0.6.6] or uninstalled
 ├─restricted by compatibility requirements with Turing [fce5fe82] to versions: 0.6.4-0.6.6
 │ └─Turing [fce5fe82] log:
 │   ├─possible versions are: [0.5.0-0.5.1, 0.6.0-0.6.2, 0.6.4-0.6.9, 0.6.11-0.6.15, 0.6.17-0.6.19, 0.6.21-0.6.23, 0.7.0-0.7.4, 0.8.0-0.8.3, 0.9.0-0.9.2, 0.10.0-0.10.1] or uninstalled
 │   └─restricted to versions 0.10.1 by an explicit requirement, leaving only versions 0.10.1
 └─restricted by compatibility requirements with Compat [34da2185] to versions: [0.1.0, 0.2.0, 0.2.5-0.2.9, 0.3.0-0.3.2, 0.4.0, 0.5.0-0.5.2] or uninstalled — no versions left
   └─Compat [34da2185] log:
     ├─possible versions are: [1.0.0-1.0.1, 1.1.0, 1.2.0, 1.3.0, 1.4.0, 1.5.0-1.5.1, 2.0.0, 2.1.0, 2.2.0, 3.0.0, 3.1.0, 3.2.0, 3.3.0-3.3.1, 3.4.0, 3.5.0, 3.6.0, 3.7.0, 3.8.0] or uninstalled
     ├─restricted by compatibility requirements with LIBSVM [b1bec4e5] to versions: [1.0.0-1.0.1, 1.1.0, 1.2.0, 1.3.0, 1.4.0, 1.5.0-1.5.1, 2.0.0, 2.1.0, 2.2.0, 3.0.0, 3.1.0, 3.2.0, 3.3.0-3.3.1, 3.4.0, 3.5.0, 3.6.0, 3.7.0, 3.8.0]
     │ └─LIBSVM [b1bec4e5] log:
     │   ├─possible versions are: [0.2.0, 0.3.0-0.3.1, 0.4.0] or uninstalled
     │   └─restricted to versions * by an explicit requirement, leaving only versions [0.2.0, 0.3.0-0.3.1, 0.4.0]
     └─restricted by compatibility requirements with Suppressor [fd094767] to versions: [1.0.0-1.0.1, 1.1.0, 1.2.0, 1.3.0, 1.4.0, 1.5.0-1.5.1, 2.0.0, 2.1.0, 2.2.0]
       └─Suppressor [fd094767] log:
         ├─possible versions are: 0.1.1 or uninstalled
         └─restricted to versions * by SpineInterface [0cda1612], leaving only versions 0.1.1
           └─SpineInterface [0cda1612] log:
             ├─possible versions are: 0.1.0 or uninstalled
             └─SpineInterface [0cda1612] is fixed to version 0.1.0

[cpfiffer]

• Remove all your packages and start from a fresh environment, by deleting everything in "C:\Users\your_username\.julia\environments\v1.4\" and then running Julia and calling ] add Turing first.

• You can use a local environment by activating the directory you are in with ] activate . and then ] add Turing.

• Try updating everything first with ] update.

• Manually go through the list of packages that are blocking your update (listed when you call ] add Turing@0.10.1) and remove them.

Did you try any of the above?

[uozden]

@cpfiffer Yes. I did all, except the first bullet point, with no success.

[cpfiffer]

The second bullet point should have solved your problem with certainty, and the fourth definitely should have, so I don't think they were done correctly. I would do the first because it is essentially fool-proof.

[uozden]

@cpfiffer, It seems the main issue is that Turing could not import MCMCChains.AbstractChains into Turing while building.

[cpfiffer]

Yes, and I have provided you numerous fixes for that problem.

[mohamed82008]

The problem is Suppressor, it is not compatible with Compat 3.x which the latest Bijectors used by the latest Turing requires.

[mohamed82008]

It seems Suppressor wasn't updated for a long time.

[uozden]

@mohamed82008 thanks for your reply. Actually it seems Suppressor updating/building as copied below. But Turing does give the same error.

  Resolving package versions...
   Updating `C:\Users\....\.julia\environments\v1.4\Project.toml`
  [fd094767] + Suppressor v0.1.1
   Updating `C:\Users\....\.julia\environments\v1.4\Manifest.toml`
 [no changes]

(@v1.4) pkg> up Suppressor
   Updating registry at `C:\Users\....\.julia\registries\General`
   Updating git-repo `https://github.com/JuliaRegistries/General.git`
   Updating `C:\Users\...\.julia\environments\v1.4\Project.toml`
 [no changes]
   Updating `C:\Users\......\.julia\environments\v1.4\Manifest.toml`
  [0bf59076] ↓ AdvancedHMC v0.2.21 ⇒ v0.2.7
  [4c555306] ↑ ArrayLayouts v0.1.5 ⇒ v0.2.0
  [aae01518] ↑ BandedMatrices v0.14.3 ⇒ v0.15.0
  [764a87c0] ↓ BoundaryValueDiffEq v2.4.0 ⇒ v2.3.0
  [781609d7] + GMP_jll v6.1.2+5
  [5078a376] ↑ LazyArrays v0.15.1 ⇒ v0.16.0
  [2ce0c516] + MPC_jll v1.1.0+0
  [3a97d323] + MPFR_jll v4.0.2+2
  [123dc426] ↑ SymEngine v0.7.1 ⇒ v0.8.0
  [3428059b] + SymEngine_jll v0.6.0+0
  [e88e6eb3] ↓ Zygote v0.4.12 ⇒ v0.4.8

(@v1.4) pkg> build Suppressor

julia> using Suppressor

(@v1.4) pkg> build Turing

[mohamed82008]

No you should remove Suppressor.

[uozden]

@mohamed82008 Thanks. removed but does not help Turing building. It seems Turing is not ready for use. I will leave it there and switch to Stan.jl

[cpfiffer]

You need to update after removing Suppressor. FYI, the problem is not Turing here, it is your package environment.