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.../libcxxwrap_julia.so: undefined symbol: small_typeof, version JL_LIBJULIA_1.10#450
@jmuchovej

Description

@jmuchovej
jmuchovej
opened on Aug 7, 2024

I trigger this specifically when trying to use VegaLite, which depends on OpenCV. I was originally using 1.10.0, but am now using 1.10.4 – I get the same errors there, that I'm reporting here.

I'm executing this in a Linux Dev Container on an M1 Macbook. Specifically, the base imagd I'm using is from Jupyter's Docker Stacks: quay.io/jupyer/datascience-notebook:2024-08-05 (previously it was the 2024-01-29 tag).

The main error I'm getting is (it repeats multiple times in the "Full Error" section below because I triggered it by attempting to precompile OpenCV. I'm unable to precompile CxxWrap OpenCV OpenCV_jll – which all trigger this error.

Not sure if this is helpful to know – but, I'm typically in a conda environment when running Julia, though Julia was installed by downloading the binary (vs using juliaup). Deactivating conda entirely doesn't appear to fix anything, though.

ERROR: LoadError: InitError: could not load library "/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so"
/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so: undefined symbol: small_typeof, version JL_LIBJULIA_1.10
Full Error 
pkg> precompile OpenCV
Precompiling OpenCV
        Info Given OpenCV was explicitly requested, output will be shown live 
ERROR: LoadError: InitError: could not load library "/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so"
/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so: undefined symbol: small_typeof, version JL_LIBJULIA_1.10
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:117
  [2] dlopen(s::String, flags::UInt32)
    @ Base.Libc.Libdl ./libdl.jl:116
  [3] macro expansion
    @ /opt/julia/packages/JLLWrappers/pG9bm/src/products/library_generators.jl:63 [inlined]
  [4] __init__()
    @ libcxxwrap_julia_jll /opt/julia/packages/libcxxwrap_julia_jll/zmDeI/src/wrappers/aarch64-linux-gnu-cxx11-julia_version+1.10.0.jl:9
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1134
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1122
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1067
  [8] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
    @ Base ./loading.jl:1581
  [9] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1938
 [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [11] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [12] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [14] macro expansion
    @ ./loading.jl:1790 [inlined]
 [15] macro expansion
    @ ./lock.jl:267 [inlined]
 [16] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [17] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [18] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [19] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
 [20] include(mod::Module, _path::String)
    @ Base ./Base.jl:495
 [21] top-level scope
    @ /opt/julia/packages/JLLWrappers/pG9bm/src/toplevel_generators.jl:192
 [22] include
    @ ./Base.jl:495 [inlined]
 [23] 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:2222
 [24] top-level scope
    @ stdin:3
during initialization of module libcxxwrap_julia_jll
in expression starting at /opt/julia/packages/OpenCV_jll/Hfsh1/src/wrappers/aarch64-linux-gnu-cxx11-julia_version+1.10.0.jl:6
in expression starting at /opt/julia/packages/OpenCV_jll/Hfsh1/src/OpenCV_jll.jl:2
in expression starting at stdin:3
ERROR: LoadError: Failed to precompile OpenCV_jll [33b9d88c-85f9-5d73-bd91-4e2b95a9aa0b] to "/opt/julia/compiled/v1.10/OpenCV_jll/jl_IbYvhS".
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:2468
  [3] compilecache
    @ ./loading.jl:2340 [inlined]
  [4] (::Base.var"#968#969"{Base.PkgId})()
    @ Base ./loading.jl:1974
  [5] mkpidlock(f::Base.var"#968#969"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia-1.10.4/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:93
  [6] #mkpidlock#6
    @ /opt/julia-1.10.4/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:88 [inlined]
  [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia-1.10.4/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:111
  [8] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
  [9] invokelatest
    @ ./essentials.jl:889 [inlined]
 [10] maybe_cachefile_lock(f::Base.var"#968#969"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:2983
 [11] maybe_cachefile_lock
    @ ./loading.jl:2980 [inlined]
 [12] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1970
 [13] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [14] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [15] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [16] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [17] macro expansion
    @ ./loading.jl:1790 [inlined]
 [18] macro expansion
    @ ./lock.jl:267 [inlined]
 [19] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [20] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [21] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [22] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
 [23] include
    @ ./Base.jl:495 [inlined]
 [24] 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:2222
 [25] top-level scope
    @ stdin:3
in expression starting at /opt/julia/packages/OpenCV/2FyNG/src/OpenCV.jl:1
in expression starting at stdin:3
  ✗ CxxWrap
  ✗ OpenCV_jll
  ✗ OpenCV
  0 dependencies successfully precompiled in 7 seconds. 43 already precompiled.

ERROR: The following 3 direct dependencies failed to precompile:

OpenCV [f878e3a2-a245-4720-8660-60795d644f2a]

Failed to precompile OpenCV [f878e3a2-a245-4720-8660-60795d644f2a] to "/opt/julia/compiled/v1.10/OpenCV/jl_WJ9BZK".
ERROR: LoadError: InitError: could not load library "/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so"
/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so: undefined symbol: small_typeof, version JL_LIBJULIA_1.10
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:117
  [2] dlopen(s::String, flags::UInt32)
    @ Base.Libc.Libdl ./libdl.jl:116
  [3] macro expansion
    @ /opt/julia/packages/JLLWrappers/pG9bm/src/products/library_generators.jl:63 [inlined]
  [4] __init__()
    @ libcxxwrap_julia_jll /opt/julia/packages/libcxxwrap_julia_jll/zmDeI/src/wrappers/aarch64-linux-gnu-cxx11-julia_version+1.10.0.jl:9
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1134
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1122
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1067
  [8] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
    @ Base ./loading.jl:1581
  [9] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1938
 [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [11] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [12] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [14] macro expansion
    @ ./loading.jl:1790 [inlined]
 [15] macro expansion
    @ ./lock.jl:267 [inlined]
 [16] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [17] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [18] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [19] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
 [20] include(mod::Module, _path::String)
    @ Base ./Base.jl:495
 [21] top-level scope
    @ /opt/julia/packages/JLLWrappers/pG9bm/src/toplevel_generators.jl:192
 [22] include
    @ ./Base.jl:495 [inlined]
 [23] 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:2222
 [24] top-level scope
    @ stdin:3
during initialization of module libcxxwrap_julia_jll
in expression starting at /opt/julia/packages/OpenCV_jll/Hfsh1/src/wrappers/aarch64-linux-gnu-cxx11-julia_version+1.10.0.jl:6
in expression starting at /opt/julia/packages/OpenCV_jll/Hfsh1/src/OpenCV_jll.jl:2
in expression starting at stdin:3
ERROR: LoadError: Failed to precompile OpenCV_jll [33b9d88c-85f9-5d73-bd91-4e2b95a9aa0b] to "/opt/julia/compiled/v1.10/OpenCV_jll/jl_IbYvhS".
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:2468
  [3] compilecache
    @ ./loading.jl:2340 [inlined]
  [4] (::Base.var"#968#969"{Base.PkgId})()
    @ Base ./loading.jl:1974
  [5] mkpidlock(f::Base.var"#968#969"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia-1.10.4/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:93
  [6] #mkpidlock#6
    @ /opt/julia-1.10.4/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:88 [inlined]
  [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia-1.10.4/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:111
  [8] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
  [9] invokelatest
    @ ./essentials.jl:889 [inlined]
 [10] maybe_cachefile_lock(f::Base.var"#968#969"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:2983
 [11] maybe_cachefile_lock
    @ ./loading.jl:2980 [inlined]
 [12] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1970
 [13] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [14] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [15] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [16] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [17] macro expansion
    @ ./loading.jl:1790 [inlined]
 [18] macro expansion
    @ ./lock.jl:267 [inlined]
 [19] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [20] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [21] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [22] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
 [23] include
    @ ./Base.jl:495 [inlined]
 [24] 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:2222
 [25] top-level scope
    @ stdin:3
in expression starting at /opt/julia/packages/OpenCV/2FyNG/src/OpenCV.jl:1
in expression starting at stdin:3
OpenCV_jll [33b9d88c-85f9-5d73-bd91-4e2b95a9aa0b]

Failed to precompile OpenCV_jll [33b9d88c-85f9-5d73-bd91-4e2b95a9aa0b] to "/opt/julia/compiled/v1.10/OpenCV_jll/jl_cAB6m6".
ERROR: LoadError: InitError: could not load library "/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so"
/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so: undefined symbol: small_typeof, version JL_LIBJULIA_1.10
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:117
  [2] dlopen(s::String, flags::UInt32)
    @ Base.Libc.Libdl ./libdl.jl:116
  [3] macro expansion
    @ /opt/julia/packages/JLLWrappers/pG9bm/src/products/library_generators.jl:63 [inlined]
  [4] __init__()
    @ libcxxwrap_julia_jll /opt/julia/packages/libcxxwrap_julia_jll/zmDeI/src/wrappers/aarch64-linux-gnu-cxx11-julia_version+1.10.0.jl:9
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1134
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1122
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1067
  [8] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
    @ Base ./loading.jl:1581
  [9] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1938
 [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [11] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [12] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [14] macro expansion
    @ ./loading.jl:1790 [inlined]
 [15] macro expansion
    @ ./lock.jl:267 [inlined]
 [16] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [17] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [18] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [19] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
 [20] include(mod::Module, _path::String)
    @ Base ./Base.jl:495
 [21] top-level scope
    @ /opt/julia/packages/JLLWrappers/pG9bm/src/toplevel_generators.jl:192
 [22] include
    @ ./Base.jl:495 [inlined]
 [23] 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:2222
 [24] top-level scope
    @ stdin:3
during initialization of module libcxxwrap_julia_jll
in expression starting at /opt/julia/packages/OpenCV_jll/Hfsh1/src/wrappers/aarch64-linux-gnu-cxx11-julia_version+1.10.0.jl:6
in expression starting at /opt/julia/packages/OpenCV_jll/Hfsh1/src/OpenCV_jll.jl:2
in expression starting at stdin:3

CxxWrap [1f15a43c-97ca-5a2a-ae31-89f07a497df4]

Failed to precompile CxxWrap [1f15a43c-97ca-5a2a-ae31-89f07a497df4] to "/opt/julia/compiled/v1.10/CxxWrap/jl_Wsjmbg".
ERROR: LoadError: InitError: could not load library "/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so"
/opt/julia/artifacts/fafe9ce52b0f6569c8d86fbb62e9d285ca9f044f/lib/libcxxwrap_julia.so: undefined symbol: small_typeof, version JL_LIBJULIA_1.10
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:117
  [2] dlopen(s::String, flags::UInt32)
    @ Base.Libc.Libdl ./libdl.jl:116
  [3] macro expansion
    @ /opt/julia/packages/JLLWrappers/pG9bm/src/products/library_generators.jl:63 [inlined]
  [4] __init__()
    @ libcxxwrap_julia_jll /opt/julia/packages/libcxxwrap_julia_jll/zmDeI/src/wrappers/aarch64-linux-gnu-cxx11-julia_version+1.10.0.jl:9
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1134
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1122
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1067
  [8] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
    @ Base ./loading.jl:1581
  [9] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1938
 [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [11] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [12] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [14] macro expansion
    @ ./loading.jl:1790 [inlined]
 [15] macro expansion
    @ ./lock.jl:267 [inlined]
 [16] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [17] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [18] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [19] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
 [20] include
    @ ./Base.jl:495 [inlined]
 [21] 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:2222
 [22] top-level scope
    @ stdin:3
during initialization of module libcxxwrap_julia_jll
in expression starting at /opt/julia/packages/CxxWrap/aXNBY/src/CxxWrap.jl:1
in expression starting at stdin:3
versioninfo 
julia> versioninfo()
Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (aarch64-linux-gnu)
  CPU: 10 × unknown
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, generic)
Threads: 10 default, 0 interactive, 5 GC (on 10 virtual cores)
Environment:
  JULIA_PROJECT = /project
  JULIA_CONDAPKG_BACKEND = Current
  JULIA_DEPOT_PATH = /opt/julia
  JULIA_NUM_THREADS = auto
  JULIA_PKGDIR = /opt/julia
/etc/os-release 
$ cat /etc/os-release 
PRETTY_NAME="Ubuntu 22.04.4 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.4 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy

I wasn't sure whether to report here on on libcxxwrap-julia. 😅

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