Issue compiling Distances.jl

[JackDunnNZ]

Trying to compile Distances gives the following error:

julia> using PackageCompiler
julia> compile_package("Distances")
...
ERROR: LoadError: LoadError: LoadError: LoadError: UndefRefError: access to undefined reference
Stacktrace:
 [1] getproperty at ./sysimg.jl:18 [inlined]
 [2] getindex at ./refvalue.jl:32 [inlined]
 [3] docm(::LineNumberNode, ::Module, ::Any) at ./docs/Docs.jl:500
 [4] @doc(::LineNumberNode, ::Module, ::Vararg{Any,N} where N) at ./boot.jl:451
 [5] include at ./boot.jl:317 [inlined]
 [6] include_relative(::Module, ::String) at ./loading.jl:1038
 [7] include at ./sysimg.jl:29 [inlined]
 [8] include(::String) at /Users/jack/.julia/packages/Distances/nLAdT/src/Distances.jl:3
 [9] top-level scope at none:0
 [10] include at ./boot.jl:317 [inlined]
 [11] include_relative(::Module, ::String) at ./loading.jl:1038
 [12] _require(::Base.PkgId) at ./loading.jl:950
 [13] require(::Base.PkgId) at ./loading.jl:852
 [14] macro expansion at ./logging.jl:311 [inlined]
 [15] require(::Module, ::Symbol) at ./loading.jl:834
 [16] top-level scope at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/sysimg/precompile.jl:4
 [17] eval(::Module, ::Any) at ./boot.jl:319
 [18] top-level scope at none:0
 [19] include at ./boot.jl:317 [inlined]
 [20] include_relative(::Module, ::String) at ./loading.jl:1038
 [21] include(::Module, ::String) at ./sysimg.jl:29
 [22] include(::String) at ./client.jl:388
 [23] top-level scope at none:0
in expression starting at /Users/jack/.julia/packages/Distances/nLAdT/src/metrics.jl:328
in expression starting at /Users/jack/.julia/packages/Distances/nLAdT/src/metrics.jl:328
in expression starting at /Users/jack/.julia/packages/Distances/nLAdT/src/Distances.jl:100
in expression starting at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/sysimg/precompile.jl:2
ERROR: failed process: Process(`/Applications/Julia-1.0.app/Contents/Resources/julia/bin/julia -Cnative -J/Users/jack/.julia/packages/PackageCompiler/Lt1dx/sysimg/backup/native/sys.dylib --compile=yes --depwarn=yes --startup-file=no --compiled-modules=no --output-o sys.a -e 'Base.__init__(); Sys.__init__() # initialize \`Base\` and \`Sys\` modules
pushfirst!(Base.DEPOT_PATH, "cache_ji_v1.0.0") # save precompiled modules locally
include("/Users/jack/.julia/packages/PackageCompiler/Lt1dx/sysimg/precompile.jl") # include Julia program file
'`, ProcessExited(1)) [1]
Stacktrace:
 [1] error(::String, ::Base.Process, ::String, ::Int64, ::String) at ./error.jl:42
 [2] pipeline_error at ./process.jl:695 [inlined]
 [3] #run#505(::Bool, ::Function, ::Cmd) at ./process.jl:653
 [4] run(::Cmd) at ./process.jl:651
 [5] (::getfield(PackageCompiler, Symbol("##4#5")))() at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/src/static_julia.jl:262
 [6] cd(::getfield(PackageCompiler, Symbol("##4#5")), ::String) at ./file.jl:96
 [7] build_object(::String, ::String, ::String, ::Bool, ::String, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing) at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/src/static_julia.jl:261
 [8] #static_julia#1(::Nothing, ::Bool, ::Bool, ::String, ::String, ::Nothing, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Bool, ::Nothing, ::Bool, ::Bool, ::String, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::typeof(static_julia), ::String) at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/src/static_julia.jl:172
 [9] #static_julia at ./none:0 [inlined]
 [10] #build_sysimg#20(::Bool, ::Bool, ::Bool, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::Nothing, ::typeof(PackageCompiler.build_sysimg), ::String, ::String) at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/src/api.jl:25
 [11] #build_sysimg at ./none:0 [inlined]
 [12] #compile_package#39(::Bool, ::Bool, ::Bool, ::Nothing, ::Function, ::Tuple{String,String}) at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/src/PackageCompiler.jl:109
 [13] compile_package at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/src/PackageCompiler.jl:103 [inlined]
 [14] #compile_package#36 at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/src/PackageCompiler.jl:92 [inlined]
 [15] compile_package(::String) at /Users/jack/.julia/packages/PackageCompiler/Lt1dx/src/PackageCompiler.jl:86
 [16] top-level scope at none:0

The error is coming from here: https://github.com/JuliaLang/julia/blob/a5bfabccd8d9c351cc3b0026992fe7314ff022db/base/docs/Docs.jl#L500

because Base.REPL_MODULE_REF is not initialized. I can fix it by adding using REPL; REPL.__init__() here: https://github.com/JuliaLang/PackageCompiler.jl/blob/master/src/static_julia.jl#L246
but I'm not sure if that's the right resolution. Thoughts?

[lucatrv]

@vtjnash can you please evaluate this? Should we add using REPL; REPL.__init__()?
Thanks

[vtjnash]

hm, that codepath was supposed to get deprecated in v1.0, so we didn't put any effort into making it correct

[JackDunnNZ]

If it helps, the problem line is:
https://github.com/JuliaStats/Distances.jl/blob/v0.7.3/src/metrics.jl#L328

[kharazity]

I'm having the same problem with that line. If you comment that line out, it should work. It's a call to create documentation. It doesn't seem essential to it's functionality. Does anyone know if there's an issue with the macro @doc?

Should be noted, that with a recent update to Distances.jl the troubling line is now 336 of metrics.jl

[dhazeghi]

Seen with current 1.1 as well.