ZygoteColorsExt interference with startup packages that load Colors.jl

[MilesCranmer]

I am struggling to make a MWE but I have encountered this problem on Julia 1.9 often enough that I'd thought I would share.

It seems like there is some interference between packages that load Colors.jl and ZygoteColorsExt.

In particular, if my startup.jl file looks like this:

# Only at replinit:
atreplinit() do repl
    @eval begin
        using ProfileView
    end
end

(ProfileView.jl loads Colors.jl)

and I activate my package DynamicExpressions.jl with ]activate DynamicExpressions.jl, which has Zygote.jl as a dependency but not Colors.jl, and then run

julia> using DynamicExpressions

I always see the following output:

[ Info: Precompiling ZygoteColorsExt [e68c091a-8ea5-5ca7-be4f-380657d4ad79]
ERROR: LoadError: ArgumentError: Package Colors [5ae59095-9a9b-59fe-a467-6f913c188581] is required but does not seem to be installed:
 - Run `Pkg.instantiate()` to install all recorded dependencies.

Stacktrace:
 [1] _require(pkg::Base.PkgId, env::String)
   @ Base ./loading.jl:1739
 [2] _require_prelocked(uuidkey::Base.PkgId, env::String)
   @ Base ./loading.jl:1625
 [3] macro expansion
   @ ./loading.jl:1613 [inlined]
 [4] macro expansion
   @ ./lock.jl:267 [inlined]
 [5] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1576
 [6] top-level scope
   @ ~/.julia/packages/Zygote/HTsWj/ext/ZygoteColorsExt.jl:5
 [7] include
   @ ./Base.jl:457 [inlined]
 [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
   @ Base ./loading.jl:2010
 [9] top-level scope
   @ stdin:2
in expression starting at /Users/mcranmer/.julia/packages/Zygote/HTsWj/ext/ZygoteColorsExt.jl:1
in expression starting at stdin:2
┌ Error: Error during loading of extension ZygoteColorsExt of Zygote, use `Base.retry_load_extensions()` to retry.
│   exception =
│    1-element ExceptionStack:
│    Failed to precompile ZygoteColorsExt [e68c091a-8ea5-5ca7-be4f-380657d4ad79] to "/Users/mcranmer/.julia/compiled/v1.9/ZygoteColorsExt/jl_GgjWAy".
│    Stacktrace:
│      [1] error(s::String)
│        @ Base ./error.jl:35
│      [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
│        @ Base ./loading.jl:2260
│      [3] compilecache
│        @ ./loading.jl:2127 [inlined]
│      [4] _require(pkg::Base.PkgId, env::Nothing)
│        @ Base ./loading.jl:1770
│      [5] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│        @ Base ./loading.jl:1625
│      [6] _require_prelocked(uuidkey::Base.PkgId)
│        @ Base ./loading.jl:1623
│      [7] run_extension_callbacks(extid::Base.ExtensionId)
│        @ Base ./loading.jl:1198
│      [8] run_extension_callbacks(pkgid::Base.PkgId)
│        @ Base ./loading.jl:1255
│      [9] run_package_callbacks(modkey::Base.PkgId)
│        @ Base ./loading.jl:1083
│     [10] _tryrequire_from_serialized(modkey::Base.PkgId, path::String, ocachepath::String, sourcepath::String, depmods::Vector{Any})
│        @ Base ./loading.jl:1363
│     [11] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
│        @ Base ./loading.jl:1459
│     [12] _require(pkg::Base.PkgId, env::String)
│        @ Base ./loading.jl:1748
│     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base ./loading.jl:1625
│     [14] macro expansion
│        @ ./loading.jl:1613 [inlined]
│     [15] macro expansion
│        @ ./lock.jl:267 [inlined]
│     [16] require(into::Module, mod::Symbol)
│        @ Base ./loading.jl:1576
│     [17] eval
│        @ ./boot.jl:370 [inlined]
│     [18] eval_user_input(ast::Any, backend::REPL.REPLBackend, mod::Module)
│        @ REPL ~/.julia/juliaup/julia-1.9.0+0.aarch64.apple.darwin14/share/julia/stdlib/v1.9/REPL/src/REPL.jl:153
│     [19] repl_backend_loop(backend::REPL.REPLBackend, get_module::Function)
│        @ REPL ~/.julia/juliaup/julia-1.9.0+0.aarch64.apple.darwin14/share/julia/stdlib/v1.9/REPL/src/REPL.jl:249
│     [20] start_repl_backend(backend::REPL.REPLBackend, consumer::Any; get_module::Function)
│        @ REPL ~/.julia/juliaup/julia-1.9.0+0.aarch64.apple.darwin14/share/julia/stdlib/v1.9/REPL/src/REPL.jl:234
│     [21] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool, backend::Any)
│        @ REPL ~/.julia/juliaup/julia-1.9.0+0.aarch64.apple.darwin14/share/julia/stdlib/v1.9/REPL/src/REPL.jl:379
│     [22] run_repl(repl::REPL.AbstractREPL, consumer::Any)
│        @ REPL ~/.julia/juliaup/julia-1.9.0+0.aarch64.apple.darwin14/share/julia/stdlib/v1.9/REPL/src/REPL.jl:365
│     [23] (::Base.var"#1017#1019"{Bool, Bool, Bool})(REPL::Module)
│        @ Base ./client.jl:421
│     [24] #invokelatest#2
│        @ ./essentials.jl:816 [inlined]
│     [25] invokelatest
│        @ ./essentials.jl:813 [inlined]
│     [26] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool)
│        @ Base ./client.jl:405
│     [27] exec_options(opts::Base.JLOptions)
│        @ Base ./client.jl:322
│     [28] _start()
│        @ Base ./client.jl:522
└ @ Base loading.jl:1204

I have tried removing my entire Julia directory, and reinstalling from scratch, but I get the same error. I haven't been able to narrow this down further.

However, if I manually add Colors.jl to my package, then everything works and the ZygoteColorsExt compiles without errors.

Furthermore, if I launch Julia with --startup-file=no, then the error goes away.

It seems to be with the fact that Colors.jl is loaded by my startup file (via ProfileView.jl), but is not in my project's Manifest.toml, which might be interfering with the extension...

[ToucheSir]

I was hoping this would be a simple case of us having the config wrong, but no such luck. Have definitely seen the error before but don't recall where. Also may have seen vaguely related ones being discussed on Slack, so maybe ask around in the Pkg-related help channels?

[MilesCranmer]

Do you think it might be a Julia bug? I guess I don't know what the correct behavior should be if a startup file loads a package whose dependencies trigger an extension to load in a local package.

It only seems to happen when Colors.jl is in my @v1.9's Manifest.toml file (and is loaded), but not in my local project's Manifest.toml file. Maybe the extension functionality of Julia is checking for loaded packages, and the Pkg part is checking the local project's Manifest.toml?

[MilesCranmer]

Another relevant observation is that if I do successfully compile it, even by temporarily adding Colors.jl to my project's Manifest.toml, then the error will not show up again. Even after I remove Colors.jl from my project's Manifest and precompile...

It is only after I delete ~/.julia/compiled/v1.9/ZygoteColorsExt does the error come back.

[MilesCranmer]

Possibly related: JuliaLang/julia#49497

[ToucheSir]

Is it possible JuliaLang/julia#49701 would fix this?

[MilesCranmer]

Perhaps. It looks like it still reads the Manifest.toml file though.

[MilesCranmer]

Okay the issue seems to go away on backports-release-1.9, so we can close this.
Thanks,
Miles