UndefRefError in docker image

[olivierlabayle]

Hi,

I am trying to build a sysimage for my project. When I do it locally it works fine, however when I try to do it in a docker image PackageCompiler crashes with the following:

create_sysimage(["TargetedEstimation"]; sysimage_path="TargetedEstimationSysimage.so")
⡆ [00m:26s] PackageCompiler: compiling incremental system imageUndefRefError: access to undefined reference
Stacktrace:
  [1] getproperty
⠇ [00m:26s] PackageCompiler: compiling incremental system imageBase.jl:37 [inlined]
  [2] getindex
    @ ./refvalue.jl:56 [inlined]
⠸ [00m:26s] PackageCompiler: compiling incremental system imageLineNumberNode, mod::Module, ex::Any)
    @ Base.Docs ./docs/Docs.jl:522
⣄ [00m:27s] PackageCompiler: compiling incremental system imageVararg{Any})
    @ Core ./boot.jl:539
  [5] #macroexpand#63
    @ ./expr.jl:119 [inlined]
  [6] macroexpand
    @ ./expr.jl:117 [inlined]
  [7] docm(source::LineNumberNode, mod::Module, meta::Any, ex::Any, define::Bool)
    @ Base.Docs ./docs/Docs.jl:539
  [8] docm(source::LineNumberNode, mod::Module, meta::Any, ex::Any)
    @ Base.Docs ./docs/Docs.jl:539
  [9] var"@doc"(::LineNumberNode, ::Module, ::String, ::Vararg{Any})
    @ Core ./boot.jl:539
 [10] include
    @ ./Base.jl:457 [inlined]
 [11] _require(pkg::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:1840
 [12] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:1660
 [13] _require_prelocked
    @ ./loading.jl:1658 [inlined]
 [14] macro expansion
    @ ./lock.jl:267 [inlined]
 [15] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1655
 [16] top-level scope
    @ /tmp/jl_feJYb05EDG:270
in expression starting at /TargetedEstimation.jl/src/TargetedEstimation.jl:48
in expression starting at /TargetedEstimation.jl/src/TargetedEstimation.jl:1
in expression starting at /tmp/jl_feJYb05EDG:270
✖ [00m:27s] PackageCompiler: compiling incremental system image
ERROR: failed process: Process(`/usr/local/julia/bin/julia --color=yes --startup-file=no --pkgimages=no --cpu-target=native --sysimage=/usr/local/julia/lib/julia/sys.so --project=/TargetedEstimation.jl --output-o=/tmp/jl_xWnQzURkpK.o /tmp/jl_feJYb05EDG`, ProcessExited(1)) [1]

Stacktrace:
  [1] pipeline_error
    @ ./process.jl:565 [inlined]
  [2] run(::Cmd; wait::Bool)
    @ Base ./process.jl:480
  [3] run
    @ ./process.jl:477 [inlined]
  [4] #19
    @ /opt/packages/PackageCompiler/Na90o/ext/TerminalSpinners.jl:157 [inlined]
  [5] spin(f::PackageCompiler.var"#19#21"{Cmd}, s::PackageCompiler.TerminalSpinners.Spinner{Base.TTY})
    @ PackageCompiler.TerminalSpinners /opt/packages/PackageCompiler/Na90o/ext/TerminalSpinners.jl:164
  [6] macro expansion
    @ /opt/packages/PackageCompiler/Na90o/ext/TerminalSpinners.jl:157 [inlined]
  [7] create_sysimg_object_file(object_file::String, packages::Vector{String}, packages_sysimg::Set{Base.PkgId}; project::String, base_sysimage::String, precompile_execution_file::Vector{String}, precompile_statements_file::Vector{String}, cpu_target::String, script::Nothing, sysimage_build_args::Cmd, extra_precompiles::String, incremental::Bool)
    @ PackageCompiler /opt/packages/PackageCompiler/Na90o/src/PackageCompiler.jl:135
  [8] create_sysimg_object_file
    @ /opt/packages/PackageCompiler/Na90o/src/PackageCompiler.jl:297 [inlined]
  [9] create_sysimage(packages::Vector{String}; sysimage_path::String, project::String, precompile_execution_file::Vector{String}, precompile_statements_file::Vector{String}, incremental::Bool, filter_stdlibs::Bool, cpu_target::String, script::Nothing, sysimage_build_args::Cmd, include_transitive_dependencies::Bool, base_sysimage::Nothing, julia_init_c_file::Nothing, julia_init_h_file::Nothing, version::Nothing, soname::Nothing, compat_level::String, extra_precompiles::String)
    @ PackageCompiler /opt/packages/PackageCompiler/Na90o/src/PackageCompiler.jl:599
 [10] top-level scope
    @ REPL[2]:1

Any idea what could be the reason and how I could debug that further?

DockerFile: https://github.com/TARGENE/TargetedEstimation.jl/blob/cv_tmle/docker/Dockerfile Julia version: 1.9.4 PackageCompiler version: 2.1.15

Many thanks!

[olivierlabayle]

It seems the error is coming from here.

REPL = Base.REPL_MODULE_REF[]

I've noticed that the first line of the script generated by PackageCompiler does Base.reinit_stdio() could it be linked? Is the REPL even accessible from the script executed to generate the sysimage object file?

[olivierlabayle]

unlikely to be duer to PackageCompiler, closing