Yes: again: "Failed to precompile due to DiffEqBase #163" about dynamicalsystems.jl

[ChrisRackauckas]

Remove ThinkJulia. Its dependencies are not updated.

[Fuffo-Lione]

Dear George,
thank you very much for your kind further explanation, which helped me to better understand where the problem might be.
Ciao
Alberto
PS And congratulations for the book you wrote !

[ChrisRackauckas]

DiffEqBase not defined? Maybe it downloaded incorrectly. What happens if you ]up and try again?

[Fuffo-Lione]

I had updated all packages this morning, but I followed your suggestion.
I have a slightly different issue sicne the list of WARNINGs is less huge :-D
Here is what I now obtain:

Info: Precompiling DynamicalSystems [61744808-ddfa-5f27-97ff-6e42cc95d634]
└ @ Base loading.jl:1664
┌ Warning: Module Distributions with build ID 52375402722901 is missing from the cache.
│ This may mean Distributions [31c24e10-a181-5473-b8eb-7969acd0382f] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1325
┌ Warning: Module Distributions with build ID 52375402722901 is missing from the cache.
│ This may mean Distributions [31c24e10-a181-5473-b8eb-7969acd0382f] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1325
┌ Info: Skipping precompilation since precompile(false). Importing DynamicalSystems [61744808-ddfa-5f27-97ff-6e42cc95d634].
└ @ Base loading.jl:1341
┌ Info: Precompiling DelayEmbeddings [5732040d-69e3-5649-938a-b6b4f237613f]
└ @ Base loading.jl:1664
┌ Warning: Module Distributions with build ID 52375402722901 is missing from the cache.
│ This may mean Distributions [31c24e10-a181-5473-b8eb-7969acd0382f] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1325
┌ Info: Skipping precompilation since precompile(false). Importing DelayEmbeddings [5732040d-69e3-5649-938a-b6b4f237613f].
└ @ Base loading.jl:1341
WARNING: method definition for DelayEmbedding at C:\Users\adono.julia\packages\DelayEmbeddings\yBNbA\src\embeddings.jl:59 declares type variable R but does not use it.
WARNING: method definition for is_stochastic at C:\Users\adono.julia\packages\DelayEmbeddings\yBNbA\src\traditional_de\automated.jl:172 declares type variable T but does not use it.
WARNING: method definition for pecuzal_multivariate_embedding_cycle! at C:\Users\adono.julia\packages\DelayEmbeddings\yBNbA\src\unified_de\pecuzal.jl:220 declares type variable D but does not use it.
┌ Info: Precompiling DynamicalSystemsBase [6e36e845-645a-534a-86f2-f5d4aa5a06b4]
└ @ Base loading.jl:1664
┌ Warning: Module DelayEmbeddings with build ID 67063813599013 is missing from the cache.
│ This may mean DelayEmbeddings [5732040d-69e3-5649-938a-b6b4f237613f] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1325
┌ Info: Skipping precompilation since precompile(false). Importing DynamicalSystemsBase [6e36e845-645a-534a-86f2-f5d4aa5a06b4].
└ @ Base loading.jl:1341
┌ Info: Precompiling SimpleDiffEq [05bca326-078c-5bf0-a5bf-ce7c7982d7fd]
└ @ Base loading.jl:1664
┌ Warning: Module DiffEqBase with build ID 52384057234601 is missing from the cache.
│ This may mean DiffEqBase [2b5f629d-d688-5b77-993f-72d75c75574e] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1325
┌ Info: Skipping precompilation since precompile(false). Importing SimpleDiffEq [05bca326-078c-5bf0-a5bf-ce7c7982d7fd].
└ @ Base loading.jl:1341
┌ Info: Precompiling Entropies [ed8fcbec-b94c-44b6-89df-898894ad9591]
└ @ Base loading.jl:1664
┌ Warning: Module DelayEmbeddings with build ID 67063813599013 is missing from the cache.
│ This may mean DelayEmbeddings [5732040d-69e3-5649-938a-b6b4f237613f] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1325
┌ Info: Skipping precompilation since precompile(false). Importing Entropies [ed8fcbec-b94c-44b6-89df-898894ad9591].
└ @ Base loading.jl:1341
┌ Info: Precompiling ChaosTools [608a59af-f2a3-5ad4-90b4-758bdf3122a7]
└ @ Base loading.jl:1664
┌ Warning: Module DelayEmbeddings with build ID 67063813599013 is missing from the cache.
│ This may mean DelayEmbeddings [5732040d-69e3-5649-938a-b6b4f237613f] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1325
┌ Info: Skipping precompilation since precompile(false). Importing ChaosTools [608a59af-f2a3-5ad4-90b4-758bdf3122a7].
└ @ Base loading.jl:1341
LoadError: UndefVarError: DiffEqBase not defined
in expression starting at C:\Users\adono.julia\packages\ChaosTools\b8DPA\src\ChaosTools.jl:1
in expression starting at C:\Users\adono.julia\packages\DynamicalSystems\quIMb\src\DynamicalSystems.jl:1

Stacktrace:
[1] include
@ .\Base.jl:419 [inlined]
[2] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1367
[3] _require_prelocked(uuidkey::Base.PkgId)
@ Base .\loading.jl:1200
[4] macro expansion
@ .\loading.jl:1180 [inlined]
[5] macro expansion
@ .\lock.jl:223 [inlined]
[6] require(into::Module, mod::Symbol)
@ Base .\loading.jl:1144
[7] include
@ .\Base.jl:419 [inlined]
[8] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1367
[9] _require_prelocked(uuidkey::Base.PkgId)
@ Base .\loading.jl:1200
[10] macro expansion
@ .\loading.jl:1180 [inlined]
[11] macro expansion
@ .\lock.jl:223 [inlined]
[12] require(into::Module, mod::Symbol)
@ Base .\loading.jl:1144
[13] eval
@ .\boot.jl:368 [inlined]
[14] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
@ Base .\loading.jl:1428

Ciao
Alberto

[ChrisRackauckas]

Show ]st. What weird unupdated package do you have in there?

[Fuffo-Lione]

As I explained in my message, I am new to Julia.
Here is the result of my ]st-ing

(@v1.8) pkg> st
Status `C:\Users\adono\.julia\environments\v1.8\Project.toml`
⌃ [2b5f629d] DiffEqBase v6.108.0
⌃ [61744808] DynamicalSystems v2.1.3
  [7073ff75] IJulia v1.23.3
  [a7f2b756] ThinkJulia v0.0.0 `https://github.com/BenLauwens/ThinkJulia.jl#master`
Info Packages marked with ⌃ have new versions available and may be upgradable. 

[Datseris]

@Fuffo-Lione please use triple quotes ``` when you paste code so that it is readable.

Latest stable, and currently frozen, version of DynamicalSystems is v2.3.2.

[Datseris]

Try to do add [email protected] to see exactly what packages hold you back.

[Fuffo-Lione]

Hi to all,
thank you for your suggestions.
I followed tham and I also went a little bit beyond
Summarizing:

1. Version 2.3.1 is the version that has been instaled this morning
2. Before trying to apply your suggestions I uninstalled Julia 1.8.2 and I installed Julia 1.8.3 , just in case
3. I added DiffeqBase
4. I tried add [email protected] but I had an error message (see below)
5. I tried add DynamicalSystems Result:: again DynamicalSystems 2.1.3 has been added
   Finally, here is what I obtained when I tried add [email protected] :

   Resolving package versions...
ERROR: Unsatisfiable requirements detected for package Colors [5ae59095]:
 Colors [5ae59095] log:
 ├─possible versions are: 0.9.0-0.12.10 or uninstalled
 ├─restricted by compatibility requirements with Reexport [189a3867] to versions: 0.12.6-0.12.10 or uninstalled, leaving only versions: 0.12.6-0.12.10
 │ └─Reexport [189a3867] log:
 │   ├─possible versions are: 0.2.0-1.2.2 or uninstalled
 │   └─restricted by compatibility requirements with IntervalRootFinding [d2bf35a9] to versions: 1.0.0-1.2.2
 │     └─IntervalRootFinding [d2bf35a9] log:
 │       ├─possible versions are: 0.4.0-0.5.10 or uninstalled
 │       └─restricted by compatibility requirements with ChaosTools [608a59af] to versions: 0.5.9-0.5.10
 │         └─ChaosTools [608a59af] log:
 │           ├─possible versions are: 0.12.0-2.9.0 or uninstalled
 │           └─restricted by compatibility requirements with DynamicalSystems [61744808] to versions: 2.9.0
 │             └─DynamicalSystems [61744808] log:
 │               ├─possible versions are: 1.0.0-2.3.2 or uninstalled
 │               └─restricted to versions 2.3.2 by an explicit requirement, leaving only versions 2.3.2
 └─restricted by compatibility requirements with ColorTypes [3da002f7] to versions: 0.9.6-0.11.2 or uninstalled — no versions left
   └─ColorTypes [3da002f7] log:
     ├─possible versions are: 0.7.0-0.11.4 or uninstalled
     ├─restricted by compatibility requirements with QuartzImageIO [dca85d43] to versions: 0.7.0-0.9.1
     │ └─QuartzImageIO [dca85d43] log:
     │   ├─possible versions are: 0.5.0-0.7.4 or uninstalled
     │   ├─restricted by compatibility requirements with Luxor [ae8d54c2] to versions: 0.5.0-0.6.0
     │   │ └─Luxor [ae8d54c2] log:
     │   │   ├─possible versions are: 0.11.0-3.6.0 or uninstalled
     │   │   └─restricted to versions 1 by ThinkJulia [a7f2b756], leaving only versions 1.0.0-1.12.0
     │   │     └─ThinkJulia [a7f2b756] log:
     │   │       ├─possible versions are: 0.0.0 or uninstalled
     │   │       └─ThinkJulia [a7f2b756] is fixed to version 0.0.0
     │   └─restricted by compatibility requirements with ColorVectorSpace [c3611d14] to versions: 0.6.0-0.7.4 or uninstalled, leaving only versions: 0.6.0
     │     └─ColorVectorSpace [c3611d14] log:
     │       ├─possible versions are: 0.6.0-0.9.9 or uninstalled
     │       ├─restricted by compatibility requirements with SpecialFunctions [276daf66] to versions: 0.8.3-0.9.9 or uninstalled
     │       │ └─SpecialFunctions [276daf66] log:
     │       │   ├─possible versions are: 0.7.0-2.1.7 or uninstalled
     │       │   ├─restricted by compatibility requirements with ChaosTools [608a59af] to versions: 0.10.0-2.1.7
     │       │   │ └─ChaosTools [608a59af] log: see above
     │       │   └─restricted by compatibility requirements with ColorVectorSpace [c3611d14] to versions: 0.7.0-1.8.7, leaving only versions: 0.10.0-1.8.7
     │       │     └─ColorVectorSpace [c3611d14] log: see above
     │       └─restricted by compatibility requirements with QuartzImageIO [dca85d43] to versions: 0.6.0-0.8.7, leaving only versions: 0.8.3-0.8.7
     │         └─QuartzImageIO [dca85d43] log: see above
     └─restricted by compatibility requirements with ColorVectorSpace [c3611d14] to versions: 0.8.0-0.10.12, leaving only versions: 0.8.0-0.9.1
       └─ColorVectorSpace [c3611d14] log: see above  ```

[Fuffo-Lione]

Hi, thank you very much: now it works.
However, I have a question: I would like to understand ; why the presence of that package infuenced so negatively the
addition and use of DynamicalSystems ?
Regards,
Alberto d'Onofrio

[ChrisRackauckas]

ThinkJulia never updated its dependencies so it has a bunch of things like "don't use dependency X beyond v0.5". v0.5 came out 4 years ago, and everything else already updated to v0.6. So in order to even have ThinkJulia in your system, you need to use packages from about the same time as Julia v1.0 came out, with many versions that aren't supported well. It's just chaos to have a package with hard bounds like that for such old things.

[Fuffo-Lione]

Hi,
Thank you.
However, I am quite amazed: how can a minor package linked to a book impede the “correct working” of a totally different recent (very interesting imho) package ? It sounds bizarre.
Have you a link where I could deepen this point ? I mean from a general viewpoint: an oldish pkg A that severely interferes with a more recent pkg Z.
I only added “ThinkJulia” a day some one month ago more or less when I wanted to evaluate that book for the course on Computer Science that I will deliver next year to the BSc students in Math my university.
Ciao
Alberto d'Onofrio (aka Fuffo-Lione)

[ChrisRackauckas]

However, I am quite amazed: how can a minor package linked to a book impede the “correct working” of a totally different recent (very interesting imho) package ? It sounds bizarre.

This happens in any language with a package system. The package literally says "please do not install anything that is recent" to the package manager. Of course that's going to cause problems. Go tell the maintainers of ThinkJulia to stop doing that and it'll go away. Most packages don't do that, I have no idea why they decided to.

[Datseris]

Alberto, I get your concern. I agree a bit; in general I would expect that you would get an older, but still working version of DynamicalSystems/DiffEq. The reason this doesn't happen here in particularly is because that ThinkJulia repo is very old and doesn't allow installing more recent versions.

But actually, antoher reason this happens is because Julia does not have yet conditional dependencies. If you go through your error messages you will see that in fact the packages that dissalow things to work together is Colors. This comes from ThinkJulia using some old versions of some plotting package. DynamicalSystems at least doesnt care about plotting, but some dependent package somewhere there does.

In the very near future, Julia will have "weak dependencies" and this will eliminate a lot of the versioning problems that comes from the dependencies on plotting packages.

[Fuffo-Lione]

Hi Chris R, I followed your suggestion and I wrote to Prof Ben Lauwens
Ciao
Alberto