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JuliaGraphs / GraphIO.jl

Graph IO functionality for various formats.
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GraphIOGraphMLExt does not support precompilation but is imported by a module that does. #57

Open dancbeaulieu opened 1 year ago

dancbeaulieu commented 1 year ago

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

MikiVanousek commented 11 months ago

I have the same issue. Does this mean I can not use the module until this is fixed?