Won't compile on fresh Julia install, complains about dependencies

[erin-atkinson]

Hi, I just installed Oceananigans, it gives this error when precompiling:

(@v1.8) pkg> precompile
Precompiling project...
✗ Oceananigans
0 dependencies successfully precompiled in 4 seconds. 146 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

Oceananigans [9e8cae18-63c1-5223-a75c-80ca9d6e9a09]

Failed to precompile Oceananigans [9e8cae18-63c1-5223-a75c-80ca9d6e9a09] to /home/yolk/.julia/compiled/v1.8/Oceananigans/jl_lpMZRF.
ERROR: LoadError: ArgumentError: Package Oceananigans does not have StaticArrays 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 Oceananigans checked out for development and have
  added StaticArrays 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 Oceananigans
  Stacktrace:
  [1] macro expansion
  @ ./loading.jl:1167 [inlined]
  [2] macro expansion
  @ ./lock.jl:223 [inlined]
  [3] require(into::Module, mod::Symbol)
  @ Base ./loading.jl:1144
  [4] include
  @ ./Base.jl:419 [inlined]
  [5] 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
  [6] top-level scope
  @ stdin:1
  in expression starting at /home/yolk/.julia/packages/Oceananigans/KClIg/src/Oceananigans.jl:1
  in expression starting at stdin:1

Tried instantiate and resolve. Here is the version info.

Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 6 × AMD Ryzen 5 4500U with Radeon Graphics
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-13.0.1 (ORCJIT, znver2)
Threads: 1 on 6 virtual cores

[glwagner]

Is this on a cluster? I've seen this before but no idea where it comes from. I've also gotten mysterious and similar errors regarding GPUArrays when trying to install CUDA.

One thing you might try is to add StaticArrays to your global environment, and the install / precompile Oceananigans. Not sure if that will help.

[glwagner]

Oddly, StaticArrays is not a direct dependency of Oceananigans:

Oceananigans.jl/Project.toml

Lines 6 to 39 in c21d5d6

	[deps]
	AMGX = "c963dde9-0319-47f5-bf0c-b07d3c80ffa6"
	Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
	AlgebraicMultigrid = "2169fc97-5a83-5252-b627-83903c6c433c"
	CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
	CUDAKernels = "72cfdca4-0801-4ab0-bf6a-d52aa10adc57"
	Crayons = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
	CubedSphere = "7445602f-e544-4518-8976-18f8e8ae6cdb"
	Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
	DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
	FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
	Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
	IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
	InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
	IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
	JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
	KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
	LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
	Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
	MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
	NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
	OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
	OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
	PencilArrays = "0e08944d-e94e-41b1-9406-dcf66b6a9d2e"
	PencilFFTs = "4a48f351-57a6-4416-9ec4-c37015456aae"
	Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
	Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
	Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
	Rotations = "6038ab10-8711-5258-84ad-4b1120ba62dc"
	SeawaterPolynomials = "d496a93d-167e-4197-9f49-d3af4ff8fe40"
	SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
	Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
	StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
	Tullio = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc"

and is not used in the Oceananigans source code. However, it is a dependency of CUDAKernels a few packages we depend on:

Oceananigans.jl/Manifest.toml

Lines 318 to 319 in c9c6e2b

	[[deps.KernelAbstractions]]
	deps = ["Adapt", "Cassette", "InteractiveUtils", "MacroTools", "SpecialFunctions", "StaticArrays", "UUIDs"]

Oceananigans.jl/Manifest.toml

Lines 82 to 83 in c9c6e2b

	[[deps.CUDAKernels]]
	deps = ["Adapt", "CUDA", "Cassette", "KernelAbstractions", "SpecialFunctions", "StaticArrays"]

Oceananigans.jl/Manifest.toml

Lines 506 to 507 in c9c6e2b

	[[deps.PencilArrays]]
	deps = ["Adapt", "ArrayInterface", "JSON3", "LinearAlgebra", "MPI", "OffsetArrays", "Random", "Reexport", "Requires", "StaticArrays", "StaticPermutations", "Strided", "TimerOutputs", "VersionParsing"]

Oceananigans.jl/Manifest.toml

Lines 576 to 577 in c9c6e2b

	[[deps.Rotations]]
	deps = ["LinearAlgebra", "Quaternions", "Random", "StaticArrays", "Statistics"]

[glwagner]

I wonder if this is related to JuliaLang/julia#42873

[erin-atkinson]

Hm.. I changed my setup a bit to avoid it (this was on Windows Subsystem for Linux, I'm just using it on Windows now). Luckily it works fine on the cluster I'm using later. If it occurs again I'll try adding the offender to the global environment but for now I'm okay.

[glwagner]

Sounds about right for this ephemeral issue! Maybe it'll get solved via this discussion sooner or later