GraphIOGraphMLExt does not support precompilation but is imported by a module that does.

ext/GraphIOGraphMLExt.jl と ext/GraphIOGEXFExt.jl から始め、次に stack trace に示されている Graphs persistence の loadgraph エントリポイントを調べます。Julia 1.9.3 でのプリコンパイル失敗と GraphML loadgraph MethodError を再現します。完了条件は、拡張機能がプリコンパイルエラーなしでロードされ、報告された GraphML 呼び出しが動作することです。

I upgraded to Julia 1.9.3 and now I can't get GraphIO to work. I am getting an error that says:

│ This may mean GraphIOGraphMLExt [357b67ce-33f7-597c-8dc9-7304118606a9] does not support precompilation but is imported by a module that does.

Error:
julia> graph = loadgraph("/home/shared/graph1.gml", GraphIO.GraphML.GraphMLFormat())
ERROR: MethodError: no method matching loadgraph(::IOStream, ::String, ::GraphIO.GraphML.GraphMLFormat)

Closest candidates are:
loadgraph(::AbstractString, ::AbstractString, ::Graphs.AbstractGraphFormat)
@ Graphs ~/.julia/packages/Graphs/FXxqo/src/persistence/common.jl:13
loadgraph(::IO, ::String, ::LGFormat)
@ Graphs ~/.julia/packages/Graphs/FXxqo/src/persistence/lg.jl:146
loadgraph(::IO, ::String, ::GraphIO.NET.NETFormat)
@ GraphIO ~/.julia/packages/GraphIO/lObxj/src/NET/Net.jl:75
...

Stacktrace:
[1] (::Graphs.var"#148#149"{String, GraphIO.GraphML.GraphMLFormat})(io::IOStream)
@ Graphs ~/.julia/packages/Graphs/FXxqo/src/persistence/common.jl:15
[2] open(::Graphs.var"#148#149"{String, GraphIO.GraphML.GraphMLFormat}, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Base ./io.jl:395
[3] open(::Function, ::String, ::String)
@ Base ./io.jl:392
[4] loadgraph(fn::String, gname::String, format::GraphIO.GraphML.GraphMLFormat)
@ Graphs ~/.julia/packages/Graphs/FXxqo/src/persistence/common.jl:14
[5] loadgraph(fn::String, format::GraphIO.GraphML.GraphMLFormat)
@ Graphs ~/.julia/packages/Graphs/FXxqo/src/persistence/common.jl:20
[6] top-level scope
@ REPL[8]:1

julia> using EzXML
│ Package EzXML not found, but a package named EzXML is available from a registry.
│ Install package?
│ (@v1.9) pkg> add EzXML
└ (y/n/o) [y]: y
Resolving package versions...
Installed EzXML ─ v1.1.0
Updating ~/.julia/environments/v1.9/Project.toml
[8f5d6c58] + EzXML v1.1.0
Updating ~/.julia/environments/v1.9/Manifest.toml
[8f5d6c58] + EzXML v1.1.0
Precompiling project...
3 dependencies successfully precompiled in 3 seconds. 138 already precompiled.
2 dependencies had warnings during precompilation:
┌ GraphIOGraphMLExt [357b67ce-33f7-597c-8dc9-7304118606a9]
│ ┌ Warning: Module GraphIOGraphMLExt with build ID ffffffff-ffff-ffff-0000-6336445ddfed is missing from the cache.
│ │ This may mean GraphIOGraphMLExt [357b67ce-33f7-597c-8dc9-7304118606a9] does not support precompilation but is imported by a module that does.
│ └ @ Base loading.jl:1793
│ ┌ Error: Error during loading of extension GraphIOGraphMLExt of GraphIO, use Base.retry_load_extensions() to retry.
│ │ exception =
│ │ 1-element ExceptionStack:
│ │ Declaring precompile(false) is not allowed in files that are being precompiled.
│ │ Stacktrace:
│ │ [1] _require(pkg::Base.PkgId, env::Nothing)
│ │ @ Base ./loading.jl:1797
│ │ [2] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│ │ @ Base ./loading.jl:1660
│ │ [3] _require_prelocked(uuidkey::Base.PkgId)
│ │ @ Base ./loading.jl:1658
│ │ [4] run_extension_callbacks(extid::Base.ExtensionId)
│ │ @ Base ./loading.jl:1255
│ │ [5] run_extension_callbacks(pkgid::Base.PkgId)
│ │ @ Base ./loading.jl:1290
│ │ [6] run_package_callbacks(modkey::Base.PkgId)
│ │ @ Base ./loading.jl:1124
│ │ [7] _require_prelocked(uuidkey::Base.PkgId, env::String)
│ │ @ Base ./loading.jl:1667
│ │ [8] macro expansion
│ │ @ ./loading.jl:1648 [inlined]
│ │ [9] macro expansion
│ │ @ ./lock.jl:267 [inlined]
│ │ [10] require(into::Module, mod::Symbol)
│ │ @ Base ./loading.jl:1611
│ │ [11] top-level scope
│ │ @ ~/.julia/packages/GraphIO/lObxj/ext/GraphIOGEXFExt.jl:8
│ │ [12] include
│ │ @ ./Base.jl:457 [inlined]
│ │ [13] 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::String)
│ │ @ Base ./loading.jl:2049
│ │ [14] top-level scope
│ │ @ stdin:3
│ │ [15] eval
│ │ @ ./boot.jl:370 [inlined]
│ │ [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│ │ @ Base ./loading.jl:1903
│ │ [17] include_string
│ │ @ ./loading.jl:1913 [inlined]
│ │ [18] exec_options(opts::Base.JLOptions)
│ │ @ Base ./client.jl:305
│ │ [19] _start()
│ │ @ Base ./client.jl:522
│ └ @ Base loading.jl:1261
└
┌ GraphIOGEXFExt [2b66b2ab-f48c-58da-9972-304391d605c5]
│ ┌ Warning: Module GraphIOGEXFExt with build ID ffffffff-ffff-ffff-0000-633643bc417c is missing from the cache.
│ │ This may mean GraphIOGEXFExt [2b66b2ab-f48c-58da-9972-304391d605c5] does not support precompilation but is imported by a module that does.
│ └ @ Base loading.jl:1793
│ ┌ Error: Error during loading of extension GraphIOGEXFExt of GraphIO, use Base.retry_load_extensions() to retry.
│ │ exception =
│ │ 1-element ExceptionStack:
│ │ Declaring precompile(false) is not allowed in files that are being precompiled.
│ │ Stacktrace:
│ │ [1] _require(pkg::Base.PkgId, env::Nothing)
│ │ @ Base ./loading.jl:1797
│ │ [2] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│ │ @ Base ./loading.jl:1660
│ │ [3] _require_prelocked(uuidkey::Base.PkgId)
│ │ @ Base ./loading.jl:1658
│ │ [4] run_extension_callbacks(extid::Base.ExtensionId)
│ │ @ Base ./loading.jl:1255
│ │ [5] run_extension_callbacks(pkgid::Base.PkgId)
│ │ @ Base ./loading.jl:1290
│ │ [6] run_package_callbacks(modkey::Base.PkgId)
│ │ @ Base ./loading.jl:1124
│ │ [7] _require_prelocked(uuidkey::Base.PkgId, env::String)
│ │ @ Base ./loading.jl:1667
│ │ [8] macro expansion
│ │ @ ./loading.jl:1648 [inlined]
│ │ [9] macro expansion
│ │ @ ./lock.jl:267 [inlined]
│ │ [10] require(into::Module, mod::Symbol)
│ │ @ Base ./loading.jl:1611
│ │ [11] top-level scope
│ │ @ ~/.julia/packages/GraphIO/lObxj/ext/GraphIOGraphMLExt.jl:8
│ │ [12] include
│ │ @ ./Base.jl:457 [inlined]
│ │ [13] 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::String)
│ │ @ Base ./loading.jl:2049
│ │ [14] top-level scope
│ │ @ stdin:3
│ │ [15] eval
│ │ @ ./boot.jl:370 [inlined]
│ │ [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│ │ @ Base ./loading.jl:1903
│ │ [17] include_string
│ │ @ ./loading.jl:1913 [inlined]
│ │ [18] exec_options(opts::Base.JLOptions)
│ │ @ Base ./client.jl:305
│ │ [19] _start()
│ │ @ Base ./client.jl:522
│ └ @ Base loading.jl:1261
└
[ Info: Precompiling GraphIOGraphMLExt [357b67ce-33f7-597c-8dc9-7304118606a9]
┌ Warning: Module GraphIOGraphMLExt with build ID ffffffff-ffff-ffff-0000-6336d9bff1e8 is missing from the cache.
│ This may mean GraphIOGraphMLExt [357b67ce-33f7-597c-8dc9-7304118606a9] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1793
┌ Error: Error during loading of extension GraphIOGraphMLExt of GraphIO, use Base.retry_load_extensions() to retry.
│ exception =
│ 1-element ExceptionStack:
│ Declaring precompile(false) is not allowed in files that are being precompiled.
│ Stacktrace:
│ [1] _require(pkg::Base.PkgId, env::Nothing)
│ @ Base ./loading.jl:1797
│ [2] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│ @ Base ./loading.jl:1660
│ [3] _require_prelocked(uuidkey::Base.PkgId)
│ @ Base ./loading.jl:1658
│ [4] run_extension_callbacks(extid::Base.ExtensionId)
│ @ Base ./loading.jl:1255
│ [5] run_extension_callbacks(pkgid::Base.PkgId)
│ @ Base ./loading.jl:1290
│ [6] run_package_callbacks(modkey::Base.PkgId)
│ @ Base ./loading.jl:1124
│ [7] _require_prelocked(uuidkey::Base.PkgId, env::String)
│ @ Base ./loading.jl:1667
│ [8] macro expansion
│ @ ./loading.jl:1648 [inlined]
│ [9] macro expansion
│ @ ./lock.jl:267 [inlined]
│ [10] require(into::Module, mod::Symbol)
│ @ Base ./loading.jl:1611
│ [11] top-level scope
│ @ ~/.julia/packages/GraphIO/lObxj/ext/GraphIOGEXFExt.jl:8
│ [12] include
│ @ ./Base.jl:457 [inlined]
│ [13] 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::String)
│ @ Base ./loading.jl:2049
│ [14] top-level scope
│ @ stdin:3
│ [15] eval
│ @ ./boot.jl:370 [inlined]
│ [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│ @ Base ./loading.jl:1903
│ [17] include_string
│ @ ./loading.jl:1913 [inlined]
│ [18] exec_options(opts::Base.JLOptions)
│ @ Base ./client.jl:305
│ [19] _start()
│ @ Base ./client.jl:522
└ @ Base loading.jl:1261