Newbie asking - How do I resolve the error: "ERROR: LoadError: ArgumentError: Package Base does not have Sobol in its dependencies"

New to Julia
1

I’m completely new to Julia, and have inherited a julia code project from another researcher. (Yay, Julia!)

I’m trying to resolve the environment, but I’m getting an error. Specifically the error says the following:

- You may have a partially installed environment. Try `Pkg.instantiate()`
  to ensure all packages in the environment are installed.
- Or, if you have Base checked out for development and have
  added Sobol as a dependency but haven't updated your primary
  environment's manifest file, try `Pkg.resolve()`.
- Otherwise you may need to report an issue with Base

Since I’m so new, I don’t want to report an issue with Base. However, I’ve followed all of the other suggested steps.

Could you help me figure out what I’m missing? Thanks in advance!

Here are my full steps:

julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.4 (2024-06-04)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

(@v1.10) pkg> 

(@v1.10) pkg> activate .
  Activating project at `~/ACAI_testing/ACAI`

(ACAI) pkg> add Sobol
   Resolving package versions...
  No Changes to `~/ACAI_testing/ACAI/Project.toml`
  No Changes to `~/ACAI_testing/ACAI/Manifest.toml`

(ACAI) pkg> up
    Updating registry at `~/.julia/registries/General.toml`
  No Changes to `~/ACAI_testing/ACAI/Project.toml`
  No Changes to `~/ACAI_testing/ACAI/Manifest.toml`

(ACAI) pkg> resolve
  No Changes to `~/ACAI_testing/ACAI/Project.toml`
  No Changes to `~/ACAI_testing/ACAI/Manifest.toml`

(ACAI) pkg> status
Project ACAI v1.5.1
Status `~/ACAI_testing/ACAI/Project.toml`
  [336ed68f] CSV v0.10.14
  [a2e0e22d] CalculusWithJulia v0.2.6
  [8f4d0f93] Conda v1.10.0
  [a93c6f00] DataFrames v1.6.1
  [31c24e10] Distributions v0.25.109
  [fde71243] EasyFit v0.6.6
  [a98d9a8b] Interpolations v0.15.1
  [033835bb] JLD2 v0.4.48
  [23992714] MAT v0.10.7
  [85f8d34a] NCDatasets v0.14.4
  [438e738f] PyCall v1.96.4
  [d330b81b] PyPlot v2.11.2
  [1fd47b50] QuadGK v2.9.4
  [ed01d8cd] Sobol v1.5.0
  [fdbf4ff8] XLSX v0.10.1
  [ddb6d928] YAML v0.4.11
  [b77e0a4c] InteractiveUtils
  [37e2e46d] LinearAlgebra
  [d6f4376e] Markdown
  [9abbd945] Profile
  [9a3f8284] Random
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0

(ACAI) pkg> precompile
Precompiling project...
        Info Given ACAI was explicitly requested, output will be shown live 
ERROR: LoadError: ArgumentError: Package Base does not have Sobol in its dependencies:
- You may have a partially installed environment. Try `Pkg.instantiate()`
  to ensure all packages in the environment are installed.
- Or, if you have Base checked out for development and have
  added Sobol as a dependency but haven't updated your primary
  environment's manifest file, try `Pkg.resolve()`.
- Otherwise you may need to report an issue with Base
Stacktrace:
 [1] macro expansion
   @ ./loading.jl:1776 [inlined]
 [2] macro expansion
   @ ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1753
 [4] #invoke_in_world#3
   @ ./essentials.jl:926 [inlined]
 [5] invoke_in_world
   @ ./essentials.jl:923 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1746
 [7] include
   @ ./Base.jl:495 [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, UInt128}}, source::Nothing)
   @ Base ./loading.jl:2222
 [9] top-level scope
   @ stdin:3
in expression starting at /home/carlau/ACAI_testing/ACAI/src/ACAI.jl:5
in expression starting at stdin:3
  ✗ ACAI
  0 dependencies successfully precompiled in 2 seconds. 182 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

ACAI [411ef148-9eb2-4e43-9147-35688f506280]

Failed to precompile ACAI [411ef148-9eb2-4e43-9147-35688f506280] to "/home/carlau/.julia/compiled/v1.10/ACAI/jl_ulyP58".
ERROR: LoadError: ArgumentError: Package Base does not have Sobol in its dependencies:
- You may have a partially installed environment. Try `Pkg.instantiate()`
  to ensure all packages in the environment are installed.
- Or, if you have Base checked out for development and have
  added Sobol as a dependency but haven't updated your primary
  environment's manifest file, try `Pkg.resolve()`.
- Otherwise you may need to report an issue with Base
Stacktrace:
 [1] macro expansion
   @ ./loading.jl:1776 [inlined]
 [2] macro expansion
   @ ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1753
 [4] #invoke_in_world#3
   @ ./essentials.jl:926 [inlined]
 [5] invoke_in_world
   @ ./essentials.jl:923 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1746
 [7] include
   @ ./Base.jl:495 [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, UInt128}}, source::Nothing)
   @ Base ./loading.jl:2222
 [9] top-level scope
   @ stdin:3
in expression starting at /home/carlau/ACAI_testing/ACAI/src/ACAI.jl:5
in expression starting at stdin:

(ACAI) pkg> instantiate

(ACAI) pkg>
2

What happens if you resolve? i.e.


(ACAI) pkg> resolve
3

Apparently nothing.

I tried @eval Base using SomePackage locally, but got an error about breaking incremental compilation, not the error you reported here.
Have you modified the base Julia environment?

4

Looks (maybe) similar to JuliaLang/julia#45832?

Is all of the code inside ACAI/src/ACAI.jl inside of a module? Does ACAI/src/ACAI.jl begin with module ACAI and end with a matched end statement? Or is there code outside of a module?

2 Likes
5

Can you post the full ACAI/src/ACAI.jl file? Or if not, can you post the first 5-10 lines or so?

6

Hi all,

Thanks for the quick response, and your willingness to help!

Here are the contents of the ACAI.jl script:

"""
ACAI: Aviation Climate and Air quality Impacts
"""
#Add packages required by ACAI
using Sobol
using Random
using YAML
using Distributions
using JLD2 
using NCDatasets
using Interpolations
using LinearAlgebra
using Statistics
using PyCall
using Base.Filesystem


#Load functions and modules to run ACAI
include("src/simulation/simulations.jl")
include("src/distribution/distributions.jl")
include("src/emission/emissions.jl")
include("src/constants/constants.jl")
include("src/output/outputs.jl")
include("src/sensitivities/sensitivities.jl")
include("src/climate/climate.jl")
include("src/airquality/airquality.jl")
include("src/main/ACAIfunctions.jl")

function runACAI(input::String)
    if !isdir("output/")
        mkdir("output/")
    end
	#read user inputs, save information in simulation variable/struct
	simulation = getSimulationInfo(input);
    #run appropriate model (advanced or original)
    if simulation.approach == "advanced" 
        emission, climateoutput, aqoutput = runACAI_adv(simulation)
        return simulation, emission, climateoutput, aqoutput
    elseif simulation.approach == "original"
        if simulation.lc_analysis
            emission, mainoutput, lcoutput = runACAI_orig(simulation)
            return simulation, emission, mainoutput, lcoutput
        else
            emission, mainoutput = runACAI_orig(simulation)
            return simulation, emission, mainoutput
        end
    end
end```
7

How do I know if I’ve modified the base environment?

I don’t think I have, but do you have a way for me to check that?

8

Hmmm, so to confirm, the text module ACAI does not currently appear anywhere in the ACAI/src/ACAI.jl file, right?

So, option 1 to try would be to add the following line at the very beginning of the ACAI/src/ACAI.jl file:

module ACAI

And also add the following line at the very end of the ACAI/src/ACAI.jl file:

end # module

Option 2 would be to leave the ACAI/src/ACAI.jl file unmodified, and instead modify the Project.toml file. Would it be possible for you to post the Project.toml file here?

3 Likes
9

Here’s the Project.toml file:

name = "ACAI"
uuid = "411ef148-9eb2-4e43-9147-35688f506280"
authors = ["joonheek "]
version = "1.5.1"

[compat]
julia = "1.10.4"       # Compatible with Julia 1.6

[deps]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
CalculusWithJulia = "a2e0e22d-7d4c-5312-9169-8b992201a882"
Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
EasyFit = "fde71243-0cda-4261-b7c7-4845bd106b21"
InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
Profile = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Sobol = "ed01d8cd-4d21-5b2a-85b4-cc3bdc58bad4"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
10

@dilumaluthge hit the nail on the head with this one I think. I was able to reproduce a similar error with that Project.toml file. But the error disappeared when I wrapped the script file in a module .... end

Try that option 1 and hopefully the issue goes away.

2 Likes