Failed to precompile Plots due to InitError in libgobject-2.0.so: undefined symbol g_pattern_spec_copy

New to Julia
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Hello all! I am getting an error when I try to run my julia project on a high-performance cluster. I installed julia v1.8.2 using conda (conda create --name myenv julia; conda activate myenv) and instantiated my project with julia --project=myproject -e "import Pkg; Pkg.instantiate()". Some of the dependencies failed to precompile, specifically:

Precompiling project...
  ✗ HTTP
  ✗ Cairo_jll
  ✗ Qt5Base_jll
  ✗ JSONSchema
  ✗ HarfBuzz_jll
  ✗ libass_jll
  ✗ Vega
  ✗ FFMPEG_jll
  ✗ VegaLite
  ✗ FFMPEG
  ✗ GR_jll
  ✗ Plots
  ✗ Patchwork
  0 dependencies successfully precompiled in 66 seconds. 189 already precompiled.

(Patchwork is the name of the project I am working on.) The stacktrace for import Pkg; Pkg.precompile() is really large. The first part also happens on my local computer, but there I can still run my program even though these modules (HTTP, JSONSchema, Vega and VegaLite) failed to precompile:

ERROR: The following 3 direct dependencies failed to precompile:

VegaLite [112f6efa-9a02-5b7d-90c0-432ed331239a]

Failed to precompile VegaLite [112f6efa-9a02-5b7d-90c0-432ed331239a] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/VegaLite/jl_6GMWif.
ERROR: LoadError: InitError: SystemError: opening file "/home/uni03/UBET/koehne19/.conda/envs/patchwork_latest/share/julia/cert.pem": No such file or directory
Stacktrace:
  [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
    @ Base ./error.jl:176
  [2] #systemerror#80
    @ ./error.jl:175 [inlined]
  [3] systemerror
    @ ./error.jl:175 [inlined]
  [4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing)
    @ Base ./iostream.jl:293
  [5] open
    @ ./iostream.jl:275 [inlined]
  [6] open(f::Base.var"#387#388"{String}, args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base ./io.jl:382
  [7] open
    @ ./io.jl:381 [inlined]
  [8] read
    @ ./io.jl:462 [inlined]
  [9] __sslinit__()
    @ MbedTLS ~/.conda/envs/patchwork_latest/share/julia/packages/MbedTLS/yELM7/src/ssl.jl:786
 [10] __init__()
    @ MbedTLS ~/.conda/envs/patchwork_latest/share/julia/packages/MbedTLS/yELM7/src/MbedTLS.jl:55
 [11] _include_from_serialized(pkg::Base.PkgId, path::String, depmods::Vector{Any})
    @ Base ./loading.jl:831
 [12] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt64)
    @ Base ./loading.jl:1039
 [13] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1315
 [14] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
 [15] macro expansion
    @ ./loading.jl:1180 [inlined]
 [16] macro expansion
    @ ./lock.jl:223 [inlined]
 [17] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
 [18] include
    @ ./Base.jl:419 [inlined]
 [19] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [20] top-level scope
    @ stdin:1
during initialization of module MbedTLS
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/HTTP/fthyG/src/HTTP.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile HTTP [cd3eb016-35fb-5094-929b-558a96fad6f3] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/HTTP/jl_myYk2A.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [inlined]
 [10] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/JSONSchema/redCi/src/JSONSchema.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile JSONSchema [7d188eb4-7ad8-530c-ae41-71a32a6d4692] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/JSONSchema/jl_R5tBLW.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [inlined]
 [10] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/Vega/WOE2W/src/Vega.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile Vega [239c3e63-733f-47ad-beb7-a12fde22c578] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/Vega/jl_BfguYI.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [inlined]
 [10] 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, UInt64}}, source::Nothing)
    @ Base ./loading.jl:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/VegaLite/F2JoW/src/VegaLite.jl:1
in expression starting at stdin:1

Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80]

Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/Plots/jl_RGfKjj.

The second part only happens on the cluster, and I have no idea what to do about it. It also happens with older julia versions like 1.7.3 and 1.7.2.

ERROR: LoadError: InitError: could not load library "/usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/artifacts/303fe895f57042ea41055187ec4af6322989b5cc/lib/libgobject-2.0.so"
/usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/artifacts/303fe895f57042ea41055187ec4af6322989b5cc/lib/libgobject-2.0.so: undefined symbol: g_pattern_spec_copy
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
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
  [4] __init__()
    @ Glib_jll ~/.conda/envs/patchwork_latest/share/julia/packages/Glib_jll/lyJkt/src/wrappers/x86_64-linux-gnu.jl:36
  [5] _include_from_serialized(pkg::Base.PkgId, path::String, depmods::Vector{Any})
    @ Base ./loading.jl:831
  [6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt64)
    @ Base ./loading.jl:1039
  [7] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1315
  [8] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [9] macro expansion
    @ ./loading.jl:1180 [inlined]
 [10] macro expansion
    @ ./lock.jl:223 [inlined]
 [11] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
 [12] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [13] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [14] include
    @ ./Base.jl:419 [inlined]
 [15] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [16] top-level scope
    @ stdin:1
during initialization of module Glib_jll
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/Cairo_jll/HW4xi/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/Cairo_jll/HW4xi/src/Cairo_jll.jl:2
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile Cairo_jll [83423d85-b0ee-5818-9007-b63ccbeb887a] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/Cairo_jll/jl_yQs1C4.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [11] include
    @ ./Base.jl:419 [inlined]
 [12] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [13] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/HarfBuzz_jll/zavaV/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/HarfBuzz_jll/zavaV/src/HarfBuzz_jll.jl:2
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile HarfBuzz_jll [2e76f6c2-a576-52d4-95c1-20adfe4de566] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/HarfBuzz_jll/jl_QfwWTu.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [11] include
    @ ./Base.jl:419 [inlined]
 [12] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [13] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/libass_jll/SaaQW/src/wrappers/x86_64-linux-gnu.jl:6
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/libass_jll/SaaQW/src/libass_jll.jl:2
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile libass_jll [0ac62f75-1d6f-5e53-bd7c-93b484bb37c0] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/libass_jll/jl_Er1rFZ.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [11] include
    @ ./Base.jl:419 [inlined]
 [12] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [13] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/FFMPEG_jll/OCtN5/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/FFMPEG_jll/OCtN5/src/FFMPEG_jll.jl:2
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/FFMPEG_jll/jl_SdZh0q.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [inlined]
 [10] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/FFMPEG/OUpap/src/FFMPEG.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile FFMPEG [c87230d0-a227-11e9-1b43-d7ebe4e7570a] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/FFMPEG/jl_AbbW26.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] include(x::String)
    @ Plots ~/.conda/envs/patchwork_latest/share/julia/packages/Plots/AAjgN/src/Plots.jl:1
 [11] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/Plots/AAjgN/src/Plots.jl:182
 [12] include
    @ ./Base.jl:419 [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, UInt64}}, source::Nothing)
    @ Base ./loading.jl:1554
 [14] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/Plots/AAjgN/src/animation.jl:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/Plots/AAjgN/src/Plots.jl:1
in expression starting at stdin:1


Patchwork [5568df11-beb6-4e3e-8878-8f1e5127fa36]

Failed to precompile Patchwork [5568df11-beb6-4e3e-8878-8f1e5127fa36] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/Patchwork/jl_8fqWnO.
ERROR: LoadError: InitError: could not load library "/usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/artifacts/303fe895f57042ea41055187ec4af6322989b5cc/lib/libgobject-2.0.so"
/usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/artifacts/303fe895f57042ea41055187ec4af6322989b5cc/lib/libgobject-2.0.so: undefined symbol: g_pattern_spec_copy
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
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
  [4] __init__()
    @ Glib_jll ~/.conda/envs/patchwork_latest/share/julia/packages/Glib_jll/lyJkt/src/wrappers/x86_64-linux-gnu.jl:36
  [5] _include_from_serialized(pkg::Base.PkgId, path::String, depmods::Vector{Any})
    @ Base ./loading.jl:831
  [6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt64)
    @ Base ./loading.jl:1039
  [7] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1315
  [8] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [9] macro expansion
    @ ./loading.jl:1180 [inlined]
 [10] macro expansion
    @ ./lock.jl:223 [inlined]
 [11] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
 [12] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [13] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [14] include
    @ ./Base.jl:419 [inlined]
 [15] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [16] top-level scope
    @ stdin:1
during initialization of module Glib_jll
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/Cairo_jll/HW4xi/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/Cairo_jll/HW4xi/src/Cairo_jll.jl:2
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile Cairo_jll [83423d85-b0ee-5818-9007-b63ccbeb887a] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/Cairo_jll/jl_ZDNthA.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [11] include
    @ ./Base.jl:419 [inlined]
 [12] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [13] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/HarfBuzz_jll/zavaV/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/HarfBuzz_jll/zavaV/src/HarfBuzz_jll.jl:2
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile HarfBuzz_jll [2e76f6c2-a576-52d4-95c1-20adfe4de566] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/HarfBuzz_jll/jl_HXfnAb.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [11] include
    @ ./Base.jl:419 [inlined]
 [12] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [13] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/libass_jll/SaaQW/src/wrappers/x86_64-linux-gnu.jl:6
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/libass_jll/SaaQW/src/libass_jll.jl:2
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile libass_jll [0ac62f75-1d6f-5e53-bd7c-93b484bb37c0] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/libass_jll/jl_k9oNgv.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [11] include
    @ ./Base.jl:419 [inlined]
 [12] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [13] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/FFMPEG_jll/OCtN5/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/FFMPEG_jll/OCtN5/src/FFMPEG_jll.jl:2
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/FFMPEG_jll/jl_fBzgT2.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include
    @ ./Base.jl:419 [inlined]
 [10] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [11] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/FFMPEG/OUpap/src/FFMPEG.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile FFMPEG [c87230d0-a227-11e9-1b43-d7ebe4e7570a] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/FFMPEG/jl_rrcMgD.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] include(x::String)
    @ Plots ~/.conda/envs/patchwork_latest/share/julia/packages/Plots/AAjgN/src/Plots.jl:1
 [11] top-level scope
    @ ~/.conda/envs/patchwork_latest/share/julia/packages/Plots/AAjgN/src/Plots.jl:182
 [12] include
    @ ./Base.jl:419 [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, UInt64}}, source::String)
    @ Base ./loading.jl:1554
 [14] top-level scope
    @ stdin:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/Plots/AAjgN/src/animation.jl:1
in expression starting at /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/packages/Plots/AAjgN/src/Plots.jl:1
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to /usr/users/koehne19/.conda/envs/patchwork_latest/share/julia/compiled/v1.8/Plots/jl_eU8sGY.
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:1707
  [3] compilecache
    @ ./loading.jl:1651 [inlined]
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1337
  [5] _require_prelocked(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1200
  [6] macro expansion
    @ ./loading.jl:1180 [inlined]
  [7] macro expansion
    @ ./lock.jl:223 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1144
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:419
 [10] include(x::String)
    @ Patchwork /scratch1/users/koehne19/patchwork_benchmarking/Patchwork/src/Patchwork.jl:4
 [11] top-level scope
    @ /scratch1/users/koehne19/patchwork_benchmarking/Patchwork/src/Patchwork.jl:92
 [12] include
    @ ./Base.jl:419 [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, UInt64}}, source::Nothing)
    @ Base ./loading.jl:1554
 [14] top-level scope
    @ stdin:1
in expression starting at /scratch1/users/koehne19/patchwork_benchmarking/Patchwork/src/plotting.jl:1

Can anybody here help me? Thank you so much.

2

On the cluster, running my program fails. So I think it has to do with the second part of the stacktrace, which seems to be related to Plots (because it’s at the “lowest end” of the stacktrace), and more specifically to Glib_jll (at the “upper end”)…

3

Please, anyone? I’m kinda desperate here, I really need to run the program on the cluster…

4

Why are you using Conda? Did some version of Julia work for you with Conda before?

I would try to download just the regular Julia, and run that way to at least rule out/or in Conda being the issue.

Well it seems to be all of them “0 dependencies successfully precompiled in 66 seconds” and I think that’s unusual, could it be some access problem, some folder read-only?!

Julia has an excellent, sufficient package manager, so why are you using Conda? I’m really curious, not sure if it often used with Julia (except when with Python, then for it). Is it out of habit? I’ve used VegaLite before (and people use all these package that should just work), I tried adding it now in my 1.8.2 just in case and got “24 dependencies successfully precompiled in 135 seconds.” for it and e.g. Vega.

5

I actually get the same issue, at least the second stacktrace box, with the regular julia 1.8.2 download… I will have a look at the access but as the Error says undefined symbol: g_pattern_spec_copy, I’m not sure how that could be an access problem.

6

I’m also having a similar error. I’m using Julia 1.7.1 as my package manager

7

@dchang10 dchang10 Can you please open a new thread providing more details about the issue you’re encountering, including the full error message, the output of the versioninfo() function and how you installed Julia?

8

For the problem with libgobject-2.0.so my educated guess is that you have in your LD_LIBRARY_PATH an old copy of glib which is being picked up by the dynamic loader. To avoid this you can start julia with

LD_LIBRARY_PATH="" julia

For the problem with the missing certificate file you’re clearly using an incomplete installation of julia.

1 Like
9

Thanks a lot! Setting LD_LIBRARY_PATH="" seems to do the trick.
As for the missing certificate file: I first installed julia using conda as shown above, but then I downloaded the tar archive from the julia site directly and that removed the problem. It seems like the julia installation is incomplete when using conda to install.

1 Like
10

Dang this fixed a lot of problems running Julia within a linux as a windows subsystem. I nulled out LD_LIBRARY_PATH in my batch script that launches Julia.

Thanks.