IJulia notebook, local Pkg activate, julia-1.7.0 FAILures

General Usage
1

Julia-1.7.0 works fine in command-line REPL after getting Pkgs installed and recompiled, but has lots of various failures when precompiling some packages with the exact same code in IJulia notebooks:

(I’ve deleted and re-created the Project.toml and Manifest.toml files in the directory to get around the failures to automatically update them, which seems to be a separate problem with julia-1.7.0.)

julia> using IJulia; notebook()
[ Info: Precompiling IJulia [7073ff75-c697-5162-941a-fcdaad2a7d2a]
[ Info: running `/usr/bin/jupyter notebook`

using Pkg
Pkg.activate(".")
Pkg.instantiate()
Pkg.status()

      Status `*******/Project.toml`
  [46ada45e] Agents v4.5.6
  [336ed68f] CSV v0.8.5
  [13f3f980] CairoMakie v0.6.6
  [a93c6f00] DataFrames v1.3.0
  [864edb3b] DataStructures v0.18.10
  [86223c79] Graphs v1.4.1
  [7073ff75] IJulia v1.23.2
  [ec714cd0] InteractiveDynamics v0.18.1
  [033835bb] JLD2 v0.4.15
  [92933f4c] ProgressMeter v1.7.1
  [ae029012] Requires v1.1.3
  [8ba89e20] Distributed
  [9a3f8284] Random

  Activating project at `*********`

using Agents

┌ Info: Precompiling Agents [46ada45e-f475-11e8-01d0-f70cc89e6671]
└ @ Base loading.jl:1423
ERROR: LoadError: too many parameters for type
Stacktrace:
 [1] _precompile_()
   @ CSV ~/.julia/packages/CSV/Zl2ww/src/precompile.jl:3
 [2] top-level scope
   @ ~/.julia/packages/CSV/Zl2ww/src/CSV.jl:49
 [3] include
   @ ./Base.jl:418 [inlined]
 [4] 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
 [5] top-level scope
   @ none:1
 [6] eval
   @ ./boot.jl:373 [inlined]
 [7] eval(x::Expr)
   @ Base.MainInclude ./client.jl:453
 [8] top-level scope
   @ none:1
in expression starting at /home/gary/.julia/packages/CSV/Zl2ww/src/CSV.jl:1
ERROR: LoadError: Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to /home/gary/.julia/compiled/v1.7/CSV/jl_5XxyIk.
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] include(x::String)
    @ Agents.AgentsIO ~/.julia/packages/Agents/HGute/src/submodules/io/AgentsIO.jl:9
  [9] top-level scope
    @ ~/.julia/packages/Agents/HGute/src/submodules/io/AgentsIO.jl:12
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
 [11] include(x::String)
    @ Agents ~/.julia/packages/Agents/HGute/src/Agents.jl:1
 [12] top-level scope
    @ ~/.julia/packages/Agents/HGute/src/Agents.jl:38
 [13] include
    @ ./Base.jl:418 [inlined]
 [14] 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
 [15] top-level scope
    @ none:1
 [16] eval
    @ ./boot.jl:373 [inlined]
 [17] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [18] top-level scope
    @ none:1
in expression starting at /home/gary/.julia/packages/Agents/HGute/src/submodules/io/csv_integration.jl:1
in expression starting at /home/gary/.julia/packages/Agents/HGute/src/submodules/io/AgentsIO.jl:3
in expression starting at /home/gary/.julia/packages/Agents/HGute/src/Agents.jl:1

Failed to precompile Agents [46ada45e-f475-11e8-01d0-f70cc89e6671] to /home/gary/.julia/compiled/v1.7/Agents/jl_vcewuX.

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] eval
   @ ./boot.jl:373 [inlined]
 [8] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
   @ Base ./loading.jl:1196
2

Here’s the IJulia-BAD-example.ipynb file:

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[32m\u001b[1m      Status\u001b[22m\u001b[39m `/media/gary/leibnizhome/gary/github/programming/julia/Agents.jl/Project.toml`\n",
      " \u001b[90m [46ada45e] \u001b[39mAgents v4.5.6\n",
      " \u001b[90m [336ed68f] \u001b[39mCSV v0.8.5\n",
      " \u001b[90m [13f3f980] \u001b[39mCairoMakie v0.6.6\n",
      " \u001b[90m [a93c6f00] \u001b[39mDataFrames v1.3.0\n",
      " \u001b[90m [864edb3b] \u001b[39mDataStructures v0.18.10\n",
      " \u001b[90m [86223c79] \u001b[39mGraphs v1.4.1\n",
      " \u001b[90m [7073ff75] \u001b[39mIJulia v1.23.2\n",
      " \u001b[90m [ec714cd0] \u001b[39mInteractiveDynamics v0.18.1\n",
      " \u001b[90m [033835bb] \u001b[39mJLD2 v0.4.15\n",
      " \u001b[90m [92933f4c] \u001b[39mProgressMeter v1.7.1\n",
      " \u001b[90m [ae029012] \u001b[39mRequires v1.1.3\n",
      " \u001b[90m [8ba89e20] \u001b[39mDistributed\n",
      " \u001b[90m [9a3f8284] \u001b[39mRandom\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001b[32m\u001b[1m  Activating\u001b[22m\u001b[39m project at `/media/gary/leibnizhome/gary/github/programming/julia/Agents.jl`\n"
     ]
    }
   ],
   "source": [
    "using Pkg\n",
    "Pkg.activate(\".\")\n",
    "Pkg.instantiate()\n",
    "Pkg.status()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "┌ Info: Precompiling Agents [46ada45e-f475-11e8-01d0-f70cc89e6671]\n",
      "└ @ Base loading.jl:1423\n",
      "\u001b[91m\u001b[1mERROR: \u001b[22m\u001b[39mLoadError: too many parameters for type\n",
      "Stacktrace:\n",
      " [1] \u001b[0m\u001b[1m_precompile_\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m   @ \u001b[39m\u001b[35mCSV\u001b[39m \u001b[90m~/.julia/packages/CSV/Zl2ww/src/\u001b[39m\u001b[90m\u001b[4mprecompile.jl:3\u001b[24m\u001b[39m\n",
      " [2] top-level scope\n",
      "\u001b[90m   @ \u001b[39m\u001b[90m~/.julia/packages/CSV/Zl2ww/src/\u001b[39m\u001b[90m\u001b[4mCSV.jl:49\u001b[24m\u001b[39m\n",
      " [3] \u001b[0m\u001b[1minclude\u001b[22m\n",
      "\u001b[90m   @ \u001b[39m\u001b[90m./\u001b[39m\u001b[90m\u001b[4mBase.jl:418\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
      " [4] \u001b[0m\u001b[1minclude_package_for_output\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mpkg\u001b[39m::\u001b[0mBase.PkgId, \u001b[90minput\u001b[39m::\u001b[0mString, \u001b[90mdepot_path\u001b[39m::\u001b[0mVector\u001b[90m{String}\u001b[39m, \u001b[90mdl_load_path\u001b[39m::\u001b[0mVector\u001b[90m{String}\u001b[39m, \u001b[90mload_path\u001b[39m::\u001b[0mVector\u001b[90m{String}\u001b[39m, \u001b[90mconcrete_deps\u001b[39m::\u001b[0mVector\u001b[90m{Pair{Base.PkgId, UInt64}}\u001b[39m, \u001b[90msource\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m   @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mloading.jl:1318\u001b[24m\u001b[39m\n",
      " [5] top-level scope\n",
      "\u001b[90m   @ \u001b[39m\u001b[90m\u001b[4mnone:1\u001b[24m\u001b[39m\n",
      " [6] \u001b[0m\u001b[1meval\u001b[22m\n",
      "\u001b[90m   @ \u001b[39m\u001b[90m./\u001b[39m\u001b[90m\u001b[4mboot.jl:373\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
      " [7] \u001b[0m\u001b[1meval\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mx\u001b[39m::\u001b[0mExpr\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m   @ \u001b[39m\u001b[90mBase.MainInclude\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mclient.jl:453\u001b[24m\u001b[39m\n",
      " [8] top-level scope\n",
      "\u001b[90m   @ \u001b[39m\u001b[90m\u001b[4mnone:1\u001b[24m\u001b[39m\n",
      "in expression starting at /home/gary/.julia/packages/CSV/Zl2ww/src/CSV.jl:1\n",
      "\u001b[91m\u001b[1mERROR: \u001b[22m\u001b[39mLoadError: Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to /home/gary/.julia/compiled/v1.7/CSV/jl_2GYGbB.\n",
      "Stacktrace:\n",
      "  [1] \u001b[0m\u001b[1merror\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90ms\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4merror.jl:33\u001b[24m\u001b[39m\n",
      "  [2] \u001b[0m\u001b[1mcompilecache\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mpkg\u001b[39m::\u001b[0mBase.PkgId, \u001b[90mpath\u001b[39m::\u001b[0mString, \u001b[90minternal_stderr\u001b[39m::\u001b[0mIO, \u001b[90minternal_stdout\u001b[39m::\u001b[0mIO, \u001b[90mignore_loaded_modules\u001b[39m::\u001b[0mBool\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mloading.jl:1466\u001b[24m\u001b[39m\n",
      "  [3] \u001b[0m\u001b[1mcompilecache\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mpkg\u001b[39m::\u001b[0mBase.PkgId, \u001b[90mpath\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mloading.jl:1410\u001b[24m\u001b[39m\n",
      "  [4] \u001b[0m\u001b[1m_require\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mpkg\u001b[39m::\u001b[0mBase.PkgId\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mloading.jl:1120\u001b[24m\u001b[39m\n",
      "  [5] \u001b[0m\u001b[1mrequire\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90muuidkey\u001b[39m::\u001b[0mBase.PkgId\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mloading.jl:1013\u001b[24m\u001b[39m\n",
      "  [6] \u001b[0m\u001b[1mrequire\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90minto\u001b[39m::\u001b[0mModule, \u001b[90mmod\u001b[39m::\u001b[0mSymbol\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mloading.jl:997\u001b[24m\u001b[39m\n",
      "  [7] \u001b[0m\u001b[1minclude\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mmod\u001b[39m::\u001b[0mModule, \u001b[90m_path\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mBase.jl:418\u001b[24m\u001b[39m\n",
      "  [8] \u001b[0m\u001b[1minclude\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mx\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[35mAgents.AgentsIO\u001b[39m \u001b[90m~/.julia/packages/Agents/HGute/src/submodules/io/\u001b[39m\u001b[90m\u001b[4mAgentsIO.jl:9\u001b[24m\u001b[39m\n",
      "  [9] top-level scope\n",
      "\u001b[90m    @ \u001b[39m\u001b[90m~/.julia/packages/Agents/HGute/src/submodules/io/\u001b[39m\u001b[90m\u001b[4mAgentsIO.jl:12\u001b[24m\u001b[39m\n",
      " [10] \u001b[0m\u001b[1minclude\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mmod\u001b[39m::\u001b[0mModule, \u001b[90m_path\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mBase.jl:418\u001b[24m\u001b[39m\n",
      " [11] \u001b[0m\u001b[1minclude\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mx\u001b[39m::\u001b[0mString\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[35mAgents\u001b[39m \u001b[90m~/.julia/packages/Agents/HGute/src/\u001b[39m\u001b[90m\u001b[4mAgents.jl:1\u001b[24m\u001b[39m\n",
      " [12] top-level scope\n",
      "\u001b[90m    @ \u001b[39m\u001b[90m~/.julia/packages/Agents/HGute/src/\u001b[39m\u001b[90m\u001b[4mAgents.jl:38\u001b[24m\u001b[39m\n",
      " [13] \u001b[0m\u001b[1minclude\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90m./\u001b[39m\u001b[90m\u001b[4mBase.jl:418\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
      " [14] \u001b[0m\u001b[1minclude_package_for_output\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mpkg\u001b[39m::\u001b[0mBase.PkgId, \u001b[90minput\u001b[39m::\u001b[0mString, \u001b[90mdepot_path\u001b[39m::\u001b[0mVector\u001b[90m{String}\u001b[39m, \u001b[90mdl_load_path\u001b[39m::\u001b[0mVector\u001b[90m{String}\u001b[39m, \u001b[90mload_path\u001b[39m::\u001b[0mVector\u001b[90m{String}\u001b[39m, \u001b[90mconcrete_deps\u001b[39m::\u001b[0mVector\u001b[90m{Pair{Base.PkgId, UInt64}}\u001b[39m, \u001b[90msource\u001b[39m::\u001b[0mNothing\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mloading.jl:1318\u001b[24m\u001b[39m\n",
      " [15] top-level scope\n",
      "\u001b[90m    @ \u001b[39m\u001b[90m\u001b[4mnone:1\u001b[24m\u001b[39m\n",
      " [16] \u001b[0m\u001b[1meval\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90m./\u001b[39m\u001b[90m\u001b[4mboot.jl:373\u001b[24m\u001b[39m\u001b[90m [inlined]\u001b[39m\n",
      " [17] \u001b[0m\u001b[1meval\u001b[22m\u001b[0m\u001b[1m(\u001b[22m\u001b[90mx\u001b[39m::\u001b[0mExpr\u001b[0m\u001b[1m)\u001b[22m\n",
      "\u001b[90m    @ \u001b[39m\u001b[90mBase.MainInclude\u001b[39m \u001b[90m./\u001b[39m\u001b[90m\u001b[4mclient.jl:453\u001b[24m\u001b[39m\n",
      " [18] top-level scope\n",
      "\u001b[90m    @ \u001b[39m\u001b[90m\u001b[4mnone:1\u001b[24m\u001b[39m\n",
      "in expression starting at /home/gary/.julia/packages/Agents/HGute/src/submodules/io/csv_integration.jl:1\n",
      "in expression starting at /home/gary/.julia/packages/Agents/HGute/src/submodules/io/AgentsIO.jl:3\n",
      "in expression starting at /home/gary/.julia/packages/Agents/HGute/src/Agents.jl:1\n"
     ]
    },
    {
     "ename": "LoadError",
     "evalue": "Failed to precompile Agents [46ada45e-f475-11e8-01d0-f70cc89e6671] to /home/gary/.julia/compiled/v1.7/Agents/jl_M9Xwji.",
     "output_type": "error",
     "traceback": [
      "Failed to precompile Agents [46ada45e-f475-11e8-01d0-f70cc89e6671] to /home/gary/.julia/compiled/v1.7/Agents/jl_M9Xwji.",
      "",
      "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] eval",
      "   @ ./boot.jl:373 [inlined]",
      " [8] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)",
      "   @ Base ./loading.jl:1196"
     ]
    }
   ],
   "source": [
    "using Agents"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "@webio": {
   "lastCommId": null,
   "lastKernelId": null
  },
  "kernelspec": {
   "display_name": "julia-1.7.0 1.7.0",
   "language": "julia",
   "name": "julia-1.7.0-1.7"
  },
  "language_info": {
   "file_extension": ".jl",
   "mimetype": "application/julia",
   "name": "julia",
   "version": "1.7.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}
3

… and here is IJulia-BAD-example.ipynb after kernel “Restart and Clear Output”:

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "using Pkg\n",
    "Pkg.activate(\".\")\n",
    "Pkg.instantiate()\n",
    "Pkg.status()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "using Agents"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "@webio": {
   "lastCommId": null,
   "lastKernelId": null
  },
  "kernelspec": {
   "display_name": "julia-1.7.0 1.7.0",
   "language": "julia",
   "name": "julia-1.7.0-1.7"
  },
  "language_info": {
   "file_extension": ".jl",
   "mimetype": "application/julia",
   "name": "julia",
   "version": "1.7.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}
4 
julia> versioninfo()
Julia Version 1.7.0
Commit 3bf9d17731 (2021-11-30 12:12 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i7-6770HQ CPU @ 2.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-12.0.1 (ORCJIT, skylake)

julia>