Updated to julia-1.10.2 giving errors with using TSML including failure during precompile

[proudindiv]

Updated to julia-1.10.2 and found several errors with using TSML including failure during precompile:
Code is copied from main TSML.jl github page: Main Workflow

• Kernel Linux 5.15.0-92-generic x86_64

• julia-1.10.2

• jupyter IJulia

• [7073ff75] IJulia v1.24.2

• [198dc43e] TSML v2.7.7

• [ Info: Precompiling TSML [198dc43e-9e51-5cd7-9d40-d9794d335912] ERROR: LoadError: InitError: UndefVarError: GR_jll not defined

• during initialization of module GRPreferences in expression starting at /home/gary/.julia/packages/Plots/HyyIK/src/init.jl:91

• ERROR: LoadError: Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to "/home/gary/.julia/compiled/v1.10/Plots/jl_9uj3Oq".

I've included the entire notebook file (with added .log for github):
TSML02workflow.ipynb.log

[ppalmes]

thanks for raising the issue. ill take a look.

[ppalmes]

Hi, I don't see any problem. Can you try these steps?

cd ./path/to/TSML.jl
julia --project
using Pkg 
Pkg.activate(".")
Pkg.instantiate()
Pkg.update()

you can also check if the unit-testing is successful or fails:

cd ./path/to/TSML.jl
julia --project
using Pkg 
Pkg.test()

[proudindiv]

I cloned TSML.jl into a clean directory and ran both your suggestions. They completed normally, without errors.

I then went to my original directory and removed the Manifest.toml and Project.toml files and re-ran my jupyter notebook that had failed. It still fails.

I then removed the *.toml files again and ran the code using the julia repl. It runs fine there.

Then I created a new notebook with julia-1.10.2 in a clean project directory, added TSML, and using TSML, and it fails as the original issue:
issue-211.ipynb.log

That seems to indicate that the problem is an incompatibility with my jupyter interface and/or IJulia.jl

As a complete neophyte in this stuff, I added NBInclude and ran the notebook from a julia repl. It failed the same way.
I'm thinking the problem may be a missing internal environment variable, but I don't know how to check that.

When I revert the new notebook to julia-1.10.1 and cleared the project, the using TSML runs fine.
issue-211.ipynb.log

Thanks for looking into the issue.

[ppalmes]

Just a note that you should not remove Project.toml because it lists the main dependencies. Manifest.toml should always be recreated based on Project.toml versions of packages so you can delete Manifest.toml and recreate it with the Pkg.instantiate() and Pkg.update(). Unfortunately, my unit-testing does not cover the jupyter notebook and focuses only on running the tests with Julia repl. You can check IJulia documentation to see if there are issues and how to install the jupyter notebook properly under the control of IJulia. If TSML runs in Julia repl without issue, most likely the issue is in IJulia or the Jupyter notebook used by IJulia.

[ppalmes]

Aside from IJulia, you can also try Pluto.jl for notebook interface.

[proudindiv]

I diffed the two log files I included, and they both list the same versions for all of the packages.
I'm using the same jupyter in both, the only difference is the julia kernal used.
When julia.1.10.1 came out, I remember I had some conflicts between the IJulia version of jupyter and the linux mint distribution version of jupyter. I think what I did was to delete both and start over with the linux distribution version. I haven't had any other problems with it since then.

I use IJulia over Pluto because it allows me to control when code cells get executed. I frequently have lots of partially completed code cells that I'm working on, and Pluto tries to execute them all the time.

I now think that this issue is probably not with the TSML package, but probably with something in the underlying plots packages.
I'll wait for the next julia version or updates to the other packages.

Again thanks for looking into it with me.

[ppalmes]

No worries. Just open another issue if you think TSML is involved. You can try running other packages with the jupyter notebook or install the Plots.jl package and see if jupyter breaks. Thanks also for reporting the issue.

[ppalmes]

By the way, if you think this is caused by the new Julia version, you may raise an issue to the Julia github. I just checked and installed IJulia with the latest kernel and it seems that the kernel fails to run. You may have found a bug with IJulia or the latest Julia.