Xubuntu 20.04 Plot install failure

Hi,
I’m looking at the possibility of using Julia as a data-processing environment. While the program (1.7.3) installs without issue, I have consistently (since (1.5.?) hit errors when attempting to install packages so that I can plot things, ideally data. Errors (after pkg.add("Plots") are

 ✗ Cairo_jll
  ✗ Qt5Base_jll
  ✗ HarfBuzz_jll
  ✗ libass_jll
  ✗ FFMPEG_jll
  ✗ FFMPEG
  ✗ GR_jll
  ✗ Plots
  125 dependencies successfully precompiled in 102 seconds
  8 dependencies errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the packages

This strikes me as something fundamental, so I am curious: What am I doing wrong? Is julia capable of plotting on linux?

Many thanks in advance,

D.

how did you install Julia

Installation procedure is

  • extract archive
  • move the archive to /usr/local
  • ln -s /usr/local/julia-1.7.3/bin/julia /usr/local/bin/julia

I test the installation by typing ‘julia’ in my home directory, then checking that 1+2 = 3 and checking that a few other examples in the early pages of the documentation. They do.

What happens if you do using Plots.

Or using GR_jll?

Hehe, yes. There is probably something special with your system.

It’s great to hear that plotting is possible in Linux. There may well be something special with my . However, I’m not using anything particularly special. Hardware’s 2014 vintage, and the installation is bog-standard.

using Plots triggers a bunch of errors as per below

julia> using Plots
[ Info: Precompiling Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80]
ERROR: LoadError: InitError: could not load library "/home/dwa/.julia/artifacts/b069ad81d556658ea64a543367e128e535fab269/lib/libgobject-2.0.so"
/home/dwa/.julia/artifacts/b069ad81d556658ea64a543367e128e535fab269/lib/libgobject-2.0.so: undefined symbol: g_uri_ref
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:117
  [3] macro expansion
    @ ~/.julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
  [4] __init__()
    @ Glib_jll ~/.julia/packages/Glib_jll/2OVnY/src/wrappers/x86_64-linux-gnu.jl:36
  [5] _include_from_serialized(path::String, depmods::Vector{Any})
    @ Base ./loading.jl:768
  [6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
    @ Base ./loading.jl:854
  [7] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1097
  [8] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [9] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
 [11] top-level scope
    @ ~/.julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [12] include
    @ ./Base.jl:418 [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:1318
 [14] top-level scope
    @ none:1
 [15] eval
    @ ./boot.jl:373 [inlined]
 [16] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [17] top-level scope
    @ none:1
during initialization of module Glib_jll
in expression starting at /home/dwa/.julia/packages/Cairo_jll/HW4xi/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /home/dwa/.julia/packages/Cairo_jll/HW4xi/src/Cairo_jll.jl:2
ERROR: LoadError: Failed to precompile Cairo_jll [83423d85-b0ee-5818-9007-b63ccbeb887a] to /home/dwa/.julia/compiled/v1.7/Cairo_jll/jl_JHWHqb.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
    @ Base ./loading.jl:1466
  [3] compilecache(pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1410
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1120
  [5] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [6] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
  [7] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
  [8] top-level scope
    @ ~/.julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
  [9] include
    @ ./Base.jl:418 [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:1318
 [11] top-level scope
    @ none:1
 [12] eval
    @ ./boot.jl:373 [inlined]
 [13] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [14] top-level scope
    @ none:1
in expression starting at /home/dwa/.julia/packages/HarfBuzz_jll/zavaV/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /home/dwa/.julia/packages/HarfBuzz_jll/zavaV/src/HarfBuzz_jll.jl:2
ERROR: LoadError: Failed to precompile HarfBuzz_jll [2e76f6c2-a576-52d4-95c1-20adfe4de566] to /home/dwa/.julia/compiled/v1.7/HarfBuzz_jll/jl_MXlrhO.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
    @ Base ./loading.jl:1466
  [3] compilecache(pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1410
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1120
  [5] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [6] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
  [7] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
  [8] top-level scope
    @ ~/.julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
  [9] include
    @ ./Base.jl:418 [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:1318
 [11] top-level scope
    @ none:1
 [12] eval
    @ ./boot.jl:373 [inlined]
 [13] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [14] top-level scope
    @ none:1
in expression starting at /home/dwa/.julia/packages/libass_jll/SaaQW/src/wrappers/x86_64-linux-gnu.jl:6
in expression starting at /home/dwa/.julia/packages/libass_jll/SaaQW/src/libass_jll.jl:2
ERROR: LoadError: Failed to precompile libass_jll [0ac62f75-1d6f-5e53-bd7c-93b484bb37c0] to /home/dwa/.julia/compiled/v1.7/libass_jll/jl_40KWXP.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
    @ Base ./loading.jl:1466
  [3] compilecache(pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1410
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1120
  [5] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [6] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
  [7] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
  [8] top-level scope
    @ ~/.julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
  [9] include
    @ ./Base.jl:418 [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:1318
 [11] top-level scope
    @ none:1
 [12] eval
    @ ./boot.jl:373 [inlined]
 [13] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [14] top-level scope
    @ none:1
in expression starting at /home/dwa/.julia/packages/FFMPEG_jll/ECokx/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /home/dwa/.julia/packages/FFMPEG_jll/ECokx/src/FFMPEG_jll.jl:2
ERROR: LoadError: Failed to precompile FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] to /home/dwa/.julia/compiled/v1.7/FFMPEG_jll/jl_NoNeFq.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
    @ Base ./loading.jl:1466
  [3] compilecache(pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1410
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1120
  [5] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [6] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
  [7] include
    @ ./Base.jl:418 [inlined]
  [8] 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:1318
  [9] top-level scope
    @ none:1
 [10] eval
    @ ./boot.jl:373 [inlined]
 [11] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [12] top-level scope
    @ none:1
in expression starting at /home/dwa/.julia/packages/FFMPEG/OUpap/src/FFMPEG.jl:1
ERROR: LoadError: Failed to precompile FFMPEG [c87230d0-a227-11e9-1b43-d7ebe4e7570a] to /home/dwa/.julia/compiled/v1.7/FFMPEG/jl_5rxxsZ.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
    @ Base ./loading.jl:1466
  [3] compilecache(pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1410
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1120
  [5] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [6] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
  [7] include
    @ ./Base.jl:418 [inlined]
  [8] 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:1318
  [9] top-level scope
    @ none:1
 [10] eval
    @ ./boot.jl:373 [inlined]
 [11] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [12] top-level scope
    @ none:1
in expression starting at /home/dwa/.julia/packages/Plots/mnkn4/src/Plots.jl:1
ERROR: Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to /home/dwa/.julia/compiled/v1.7/Plots/jl_zgIKz3.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
   @ Base ./loading.jl:1466
 [3] compilecache(pkg::Base.PkgId, path::String)
   @ Base ./loading.jl:1410
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1120
 [5] require(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1013
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:997

using GR_jll says that the package is not installed, and offers to install it. Allowing julia to proceed with the installation triggers the mess below:

julia> using GR_jll
 │ Package GR_jll not found, but a package named GR_jll is available from a registry. 
 │ Install package?
 │   (@v1.7) pkg> add GR_jll 
 └ (y/n) [y]: y
   Resolving package versions...
    Updating `~/.julia/environments/v1.7/Project.toml`
  [d2c73de3] + GR_jll v0.64.4+0
  No Changes to `~/.julia/environments/v1.7/Manifest.toml`
[ Info: Precompiling GR_jll [d2c73de3-f751-5644-a686-071e5b155ba9]
ERROR: LoadError: InitError: could not load library "/home/dwa/.julia/artifacts/b069ad81d556658ea64a543367e128e535fab269/lib/libgobject-2.0.so"
/home/dwa/.julia/artifacts/b069ad81d556658ea64a543367e128e535fab269/lib/libgobject-2.0.so: undefined symbol: g_uri_ref
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:117
  [3] macro expansion
    @ ~/.julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
  [4] __init__()
    @ Glib_jll ~/.julia/packages/Glib_jll/2OVnY/src/wrappers/x86_64-linux-gnu.jl:36
  [5] _include_from_serialized(path::String, depmods::Vector{Any})
    @ Base ./loading.jl:768
  [6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
    @ Base ./loading.jl:854
  [7] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1097
  [8] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [9] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
 [11] top-level scope
    @ ~/.julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
 [12] include
    @ ./Base.jl:418 [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:1318
 [14] top-level scope
    @ none:1
 [15] eval
    @ ./boot.jl:373 [inlined]
 [16] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [17] top-level scope
    @ none:1
during initialization of module Glib_jll
in expression starting at /home/dwa/.julia/packages/Cairo_jll/HW4xi/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at /home/dwa/.julia/packages/Cairo_jll/HW4xi/src/Cairo_jll.jl:2
ERROR: LoadError: Failed to precompile Cairo_jll [83423d85-b0ee-5818-9007-b63ccbeb887a] to /home/dwa/.julia/compiled/v1.7/Cairo_jll/jl_4UNTBk.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
    @ Base ./loading.jl:1466
  [3] compilecache(pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1410
  [4] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1120
  [5] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [6] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
  [7] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
  [8] top-level scope
    @ ~/.julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
  [9] include
    @ ./Base.jl:418 [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:1318
 [11] top-level scope
    @ none:1
 [12] eval
    @ ./boot.jl:373 [inlined]
 [13] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [14] top-level scope
    @ none:1
in expression starting at /home/dwa/.julia/packages/GR_jll/HZlFL/src/wrappers/x86_64-linux-gnu-cxx11.jl:5
in expression starting at /home/dwa/.julia/packages/GR_jll/HZlFL/src/GR_jll.jl:2
ERROR: Failed to precompile GR_jll [d2c73de3-f751-5644-a686-071e5b155ba9] to /home/dwa/.julia/compiled/v1.7/GR_jll/jl_BTBMq2.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
   @ Base ./loading.jl:1466
 [3] compilecache(pkg::Base.PkgId, path::String)
   @ Base ./loading.jl:1410
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1120
 [5] require(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1013
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:997

where I’d note failure to compile Cairo_jll & GR_jll.

Is there another plotting package that should be used instead of Plots?

D.

Are you setting some env variable like LD_LIBRARY_PATH that could mess up library loading?

Try running LD_LIBRARY_PATH="" julia and see what happens:

Here are some related issues:

https://github.com/JuliaGraphics/Gtk.jl/issues/588

1 Like

Well that seemed to have fixed the issue.

Clearing LD_LIBRARY_PATH, then starting julia and running through the first few examples in the Plots tutorial produced the expected output.

Many thanks for your help!

D.

1 Like

In general, LD_LIBRARY_PATH is a pretty bad idea to use due to problems like this. You are overriding the normal linking behaviors so clearly, any library that now uses the wrong version of its dependency can error in pretty much arbitrary ways.