Homebrew's Julia Build is not built correctly and causes package precompilation errors #271

SvenDuve · 2023-02-06T12:36:44Z

Hello,

I can't precompile DifferentialEquations pointing me to an issue with LinearSolve, and several other packages( Also not pre-compiling: StochasticDiffEq.jl, OrdinaryDiffEq.jl).

I was trying to add the package standalone, and got the following:

julia> using LinearSolve │ Package LinearSolve not found, but a package named LinearSolve is available │ from a registry. │ Install package? │ (@v1.8) pkg> add LinearSolve └ (y/n/o) [y]: y Updating registry at ~~/.julia/registries/General.tomlResolving package versions... Updating~~/.julia/environments/v1.8/Project.toml[7ed4a6bd] + LinearSolve v1.35.0 No Changes to~/.julia/environments/v1.8/Manifest.toml`
[ Info: Precompiling LinearSolve [7ed4a6bd-45f5-4d41-b270-4a48e9bafcae]
ERROR: LoadError: MethodError: convert(::Type{Union{}}, ::SparseArrays.SparseMatrixCSC{Float64, Int64}) is ambiguous. Candidates:
convert(T::Type{<:LinearAlgebra.Bidiagonal}, m::AbstractMatrix) in LinearAlgebra at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/LinearAlgebra/src/bidiag.jl:203
convert(T::Type{<:SparseArrays.AbstractSparseMatrixCSC}, m::AbstractMatrix) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:745
convert(T::Type{<:LinearAlgebra.SymTridiagonal}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:749
convert(T::Type{<:LinearAlgebra.LowerTriangular}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:753
convert(T::Type{<:SparseArrays.SparseVector}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsevector.jl:466
convert(T::Type{<:LinearAlgebra.Tridiagonal}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:751
convert(T::Type{<:LinearAlgebra.UpperTriangular}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:755
convert(T::Type{<:LinearAlgebra.Diagonal}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:747
convert(::Type{Union{}}, a::AbstractArray) in Base at array.jl:618
convert(::Type{SA}, a::AbstractArray) where SA<:StaticArraysCore.StaticArray in StaticArrays at /Users/svenduve/.julia/packages/StaticArrays/jA1zK/src/convert.jl:194
convert(::Type{T}, a::AbstractArray) where T<:Array in Base at array.jl:617
convert(T::Type{<:BitArray}, a::AbstractArray) in Base at bitarray.jl:580
convert(::Type{T}, M::AbstractArray) where T<:OffsetArrays.OffsetArray in OffsetArrays at /Users/svenduve/.julia/packages/OffsetArrays/TcCEq/src/OffsetArrays.jl:256
convert(::Type{Union{}}, x) in Base at essentials.jl:213
convert(::Type{T}, obj) where T<:FunctionWrappers.FunctionWrapper in FunctionWrappers at /Users/svenduve/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:113
convert(::Type{T}, arg) where T<:VecElement in Base at baseext.jl:19
Possible fix, define
convert(::Type{Union{}}, ::SparseArrays.AbstractSparseMatrixCSC)
Stacktrace:
[1] Sparspak.SpkSparseSolver.SparseSolver{Int64, Float64}(p::SparseArrays.SparseMatrixCSC{Float64, Int64}, slvr::Sparspak.SpkSparseBase._SparseBase{Int64, Float64}, n::Int64, ma::Int64, na::Int64, mc::Int64, nc::Int64, _inmatrixdone::Bool, _orderdone::Bool, _symbolicdone::Bool, _factordone::Bool, _trisolvedone::Bool, _refinedone::Bool, _condestdone::Bool) (repeats 2 times)
@ Sparspak.SpkSparseSolver ~/.julia/packages/Sparspak/5cKXy/src/SparseMethod/SpkSparseSolver.jl:18
[2] Sparspak.SpkSparseSolver.SparseSolver(m::SparseArrays.SparseMatrixCSC{Float64, Int64})
@ Sparspak.SparseCSCInterface ~/.julia/packages/Sparspak/5cKXy/src/SparseCSCInterface/SparseCSCInterface.jl:189
[3] sparspaklu(m::SparseArrays.SparseMatrixCSC{Float64, Int64}; factorize::Bool)
@ Sparspak.SparseCSCInterface ~/.julia/packages/Sparspak/5cKXy/src/SparseCSCInterface/SparseCSCInterface.jl:219
[4] init_cacheval(#unused#::LinearSolve.SparspakFactorization, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, b::Vector{Float64}, u::Vector{Float64}, Pl::SciMLOperators.IdentityOperator{4}, Pr::SciMLOperators.IdentityOperator{4}, maxiters::Int64, abstol::Float64, reltol::Float64, verbose::Bool, assumptions::LinearSolve.OperatorAssumptions{true})
@ LinearSolve ~/.julia/packages/LinearSolve/fBayl/src/factorization.jl:514
[5] init(::SciMLBase.LinearProblem{Nothing, true, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}, SciMLBase.NullParameters, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, ::LinearSolve.SparspakFactorization; alias_A::Bool, alias_b::Bool, abstol::Float64, reltol::Float64, maxiters::Int64, verbose::Bool, Pl::SciMLOperators.IdentityOperator{4}, Pr::SciMLOperators.IdentityOperator{4}, assumptions::LinearSolve.OperatorAssumptions{true}, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ LinearSolve ~/.julia/packages/LinearSolve/fBayl/src/common.jl:117
[6] init(::SciMLBase.LinearProblem{Nothing, true, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}, SciMLBase.NullParameters, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, ::LinearSolve.SparspakFactorization)
@ LinearSolve ~/.julia/packages/LinearSolve/fBayl/src/common.jl:88
[7] solve(::SciMLBase.LinearProblem{Nothing, true, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}, SciMLBase.NullParameters, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, ::LinearSolve.SparspakFactorization; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ LinearSolve ~/.julia/packages/LinearSolve/fBayl/src/common.jl:157
[8] solve(::SciMLBase.LinearProblem{Nothing, true, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}, SciMLBase.NullParameters, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, ::LinearSolve.SparspakFactorization)
@ LinearSolve ~/.julia/packages/LinearSolve/fBayl/src/common.jl:154
[9] macro expansion
@ ~/.julia/packages/LinearSolve/fBayl/src/LinearSolve.jl:102 [inlined]
[10] top-level scope
@ ~/.julia/packages/SnoopPrecompile/1XXT1/src/SnoopPrecompile.jl:62
[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::Nothing)
@ Base ./loading.jl:1554
[13] top-level scope
@ stdin:1
in expression starting at /Users/svenduve/.julia/packages/LinearSolve/fBayl/src/LinearSolve.jl:1
in expression starting at stdin:1
ERROR: Failed to precompile LinearSolve [7ed4a6bd-45f5-4d41-b270-4a48e9bafcae] to /Users/svenduve/.julia/compiled/v1.8/LinearSolve/jl_FFaxJU.
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

`

I am on Julia 1.8.5, just updated.

Many thanks.

The text was updated successfully, but these errors were encountered:

ChrisRackauckas · 2023-02-06T12:41:22Z

Can you share versioninfo()? It looks like it might be the same as https://discourse.julialang.org/t/precompile-error-in-differentialequations-jl/94086/5 and #266, which might only be on Mac M1? So versioninfo() would be helpful because this also looks to be the same, and it looks to be the Homebrew build?

SvenDuve · 2023-02-06T12:59:09Z

julia> versioninfo() Julia Version 1.8.5 Commit 17cfb8e65e* (2023-01-08 06:45 UTC) Platform Info: OS: macOS (arm64-apple-darwin22.1.0) CPU: 10 × Apple M1 Pro WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1) Threads: 1 on 8 virtual cores

, and yes its a home-brew build.

is M1 an issue?

ChrisRackauckas · 2023-02-06T13:30:37Z

Looks like it might be. I'll need to track down someone who has one. @YingboMa @chriselrod have you experienced this?

j-fu · 2023-02-06T13:52:15Z

I found a colleague, he had no problem.

ChrisRackauckas · 2023-02-06T14:03:13Z

Was it the homebrew version?

chriselrod · 2023-02-06T14:39:51Z

The error is:

[ Info: Precompiling LinearSolve [7ed4a6bd-45f5-4d41-b270-4a48e9bafcae]
ERROR: LoadError: MethodError: convert(::Type{Union{}}, ::SparseArrays.SparseMatrixCSC{Float64, Int64}) is ambiguous. Candidates:
convert(T::Type{<:LinearAlgebra.Bidiagonal}, m::AbstractMatrix) in LinearAlgebra at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/LinearAlgebra/src/bidiag.jl:203
convert(T::Type{<:SparseArrays.AbstractSparseMatrixCSC}, m::AbstractMatrix) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:745
convert(T::Type{<:LinearAlgebra.SymTridiagonal}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:749
convert(T::Type{<:LinearAlgebra.LowerTriangular}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:753
convert(T::Type{<:SparseArrays.SparseVector}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsevector.jl:466
convert(T::Type{<:LinearAlgebra.Tridiagonal}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:751
convert(T::Type{<:LinearAlgebra.UpperTriangular}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:755
convert(T::Type{<:LinearAlgebra.Diagonal}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:747
convert(::Type{Union{}}, a::AbstractArray) in Base at array.jl:618
convert(::Type{SA}, a::AbstractArray) where SA<:StaticArraysCore.StaticArray in StaticArrays at /Users/svenduve/.julia/packages/StaticArrays/jA1zK/src/convert.jl:194
convert(::Type{T}, a::AbstractArray) where T<:Array in Base at array.jl:617
convert(T::Type{<:BitArray}, a::AbstractArray) in Base at bitarray.jl:580
convert(::Type{T}, M::AbstractArray) where T<:OffsetArrays.OffsetArray in OffsetArrays at /Users/svenduve/.julia/packages/OffsetArrays/TcCEq/src/OffsetArrays.jl:256
convert(::Type{Union{}}, x) in Base at essentials.jl:213
convert(::Type{T}, obj) where T<:FunctionWrappers.FunctionWrapper in FunctionWrappers at /Users/svenduve/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:113
convert(::Type{T}, arg) where T<:VecElement in Base at baseext.jl:19
Possible fix, define
convert(::Type{Union{}}, ::SparseArrays.AbstractSparseMatrixCSC)

Union{} looks wrong, so I'll have to check where that came from.

I'm always suspicious of Julia installs that aren't official binaries/from juliaup/built from source.
This at least isn't an error complaining about llvm or a random segfault.

Union{} looks like someone used Base.promote_op/Core.compiler.return_type to pick a type to convert to (or container eltype), but the function signature hit something that does not return/is known to error.
Which maybe could be related.
I'll try on my M1 soon.

ChrisRackauckas · 2023-02-06T14:41:51Z

We've got a dev recreating the error, finally 😅😅😅😅😅😅😅😅😅

j-fu · 2023-02-06T14:48:06Z

It went well on my colleague's M1 with homebrew 3.6.14.

Yeah Union{} of course looks wrong. It is in an assignement of a struct element declared as

p::Union{Problem{IT, FT},SparseMatrixCSC{FT,IT}}

chriselrod · 2023-02-06T14:51:51Z

No, I copy/pasted from above to make it readable lol
I don't have a problem with LinearSolve myself...

julia> using LinearSolve
 │ Package LinearSolve not found, but a package named LinearSolve is available from a registry. 
 │ Install package?
 │   (diffeq) pkg> add LinearSolve 
 └ (y/n/o) [y]: 
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
    Updating `~/Documents/progwork/julia/env/diffeq/Project.toml`
  [7ed4a6bd] + LinearSolve v1.35.0
  No Changes to `~/Documents/progwork/julia/env/diffeq/Manifest.toml`

julia> versioninfo()
Julia Version 1.10.0-DEV.501
Commit 2a9f4412a0 (2023-02-05 19:46 UTC)
Platform Info:
  OS: Linux (aarch64-unknown-linux-gnu)
  CPU: 8 × unknown
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1)
  Threads: 8 on 8 virtual cores
Environment:
  JULIA_PATH = @.
  JULIA_NUM_THREADS = 8

(diffeq) pkg> st -m LinearSolve
Status `~/Documents/progwork/julia/env/diffeq/Manifest.toml`
  [7ed4a6bd] LinearSolve v1.35.0

ChrisRackauckas · 2023-02-06T14:52:47Z

...

chriselrod · 2023-02-06T15:00:06Z

It went well on my colleague's M1 with homebrew 3.6.14.

Yeah Union{} of course looks wrong. It is in an assignement of a struct element declared as

p::Union{Problem{IT, FT},SparseMatrixCSC{FT,IT}}

I can't think of many ways for Union{} to appear, and can't think of any from this. Trying to play with minimal examples, things seem to behave as I'd expect:

julia> struct FooUnion
           x::Union{Float64,Int64}
       end

julia> FooUnion(1f0) # calls convert(::Type{Union{Float64, Int64}}, x::Float32)
ERROR: MethodError: no method matching Union{Float64, Int64}(::Float32)

Closest candidates are:
  (::Type{T})(::T) where T<:Number
   @ Core boot.jl:793
  (::Type{T})(::Base.TwicePrecision) where T<:Number
   @ Base twiceprecision.jl:266
  (::Type{T})(::Complex) where T<:Real
   @ Base complex.jl:44
  ...

Stacktrace:
 [1] convert(#unused#::Type{Union{Float64, Int64}}, x::Float32)
   @ Base ./number.jl:7
 [2] FooUnion(x::Float32)
   @ Main ./REPL[2]:2
 [3] top-level scope
   @ REPL[3]:1

julia> struct FooUnion1
           x::Union{AbstractFloat,Nothing}
``
       end

julia> FooUnion1(1f0)
FooUnion1(1.0f0)

julia> FooUnion1(nothing)
FooUnion1(nothing)

julia> FooUnion1(false) # promotes to float
FooUnion1(0.0)

SparseArrays.SparseMatrixCSC{Float64, Int64}) should have no problem being assigned to a p::Union{Problem{IT, FT},SparseMatrixCSC{FT,IT}} field.

Mind running ] st -m LinearSolve Sparspak?

j-fu · 2023-02-06T15:03:42Z

Other OP is on https://discourse.julialang.org/t/precompile-error-in-differentialequations-jl/94086/11

j-fu · 2023-02-06T15:05:22Z

Yeah this already goes through all kinds of CI on win/mac(intel)/linux. So this appears really wild to me.

jredondoyuste · 2023-02-06T15:06:45Z

Hi! Other person with the issue here: my Homebrew is 3.6.20, that's how I built Julia

SvenDuve · 2023-02-06T15:53:14Z

I am on Homebrew 3.6.20 FYI.

I'll remove the Homebrew install and try the official binary now.

SvenDuve · 2023-02-06T16:07:25Z

right, that has worked:

julia> versioninfo()

Julia Version 1.8.5 Commit 17cfb8e65ea (2023-01-08 06:45 UTC) Platform Info: OS: macOS (arm64-apple-darwin21.5.0) CPU: 10 × Apple M1 Pro WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1) Threads: 1 on 8 virtual cores

then using the already installed Package...

julia> using LinearSolve

[ Info: Precompiling LinearSolve [7ed4a6bd-45f5-4d41-b270-4a48e9bafcae] ┌ Warning: Replacing docs for 'SciMLOperators.AbstractSciMLOperator :: Union{}' in module 'SciMLOperators' └ @ Base.Docs docs/Docs.jl:240 ┌ Warning: Replacing docs for 'SciMLBase.sol :: Union{Tuple, Tuple{D}, Tuple{S}, Tuple{N}, Tuple{T}} where {T, N, S, D}' in module 'SciMLBase' └ @ Base.Docs docs/Docs.jl:240

YingboMa · 2023-02-06T16:20:03Z

Is the issue not resolved?

chriselrod · 2023-02-06T16:27:34Z

Has anyone reported this problem not been on a Homebrew Julia?

Also

[ Info: Precompiling LinearSolve [7ed4a6bd-45f5-4d41-b270-4a48e9bafcae] ┌ Warning: Replacing docs for 'SciMLOperators.AbstractSciMLOperator :: Union{}' in module 'SciMLOperators' └ @ Base.Docs docs/Docs.jl:240

Union{}...?

YingboMa · 2023-02-06T16:28:48Z

Nothing a little rm -rf ~/.julia/compiled/ cannot fix.

chriselrod · 2023-02-06T16:29:49Z

Shouldn't their old compiled be ignored now that they have a different julia?

jredondoyuste · 2023-02-06T18:22:33Z

Uninstalling the Brew build and installing from source works for me perfectly fine, now :)

thanks for the help!

chriselrod · 2023-02-06T21:58:10Z

Should we just point to everyone running into this to either install an official binary, use juliaup, or build from source?

Supposedly homebrew isn't like some of the bad distributors that ship Julia with unpatched dependencies, so presumably they'd be interested in knowing what's going wrong and fixing it.

j-fu · 2023-02-06T23:56:06Z

Guess yes, I understand that the official binary is almost always the better choice (BTW after starting with the openSUSE build fora while)...

OTOH yeah - someone invested in the homebrew stuff might alert them...

EDIT: There seems to be a quite subtle issue behind this. I would understand if this would be floating point stuff and the rounding goes the other direction, but this one isn't. So my gut feeling is that it is really worth to dig down.

philippemiron · 2023-02-25T02:29:04Z

Someone knows what's wrong with the Homebrew version? It does look like it's getting the binary from official sources.

https://github.com/Homebrew/homebrew-cask/blob/efbe1ed540f7a51335ff78c8232a3f06835a7cb8/Casks/julia.rb

Fedster · 2023-04-17T08:22:21Z

Does not work for me. Homebrew Julia, some info:

brew --version
Homebrew 4.0.13

julia versioninfo()
Julia Version 1.8.5
Commit 17cfb8e65e* (2023-01-08 06:45 UTC)
Platform Info:
OS: macOS (arm64-apple-darwin22.1.0)
CPU: 10 × Apple M1 Max
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1)
Threads: 1 on 8 virtual cores

error

using LinearSolve
[ Info: Precompiling LinearSolve [7ed4a6bd-45f5-4d41-b270-4a48e9bafcae]
ERROR: LoadError: MethodError: convert(::Type{Union{}}, ::SparseArrays.SparseMatrixCSC{Float64, Int64}) is ambiguous. Candidates:
convert(T::Type{<:LinearAlgebra.Bidiagonal}, m::AbstractMatrix) in LinearAlgebra at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/LinearAlgebra/src/bidiag.jl:203
convert(T::Type{<:SparseArrays.AbstractSparseMatrixCSC}, m::AbstractMatrix) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:745
convert(T::Type{<:LinearAlgebra.SymTridiagonal}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:749
convert(T::Type{<:LinearAlgebra.LowerTriangular}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:753
convert(T::Type{<:SparseArrays.SparseVector}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsevector.jl:466
convert(T::Type{<:LinearAlgebra.Tridiagonal}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:751
convert(T::Type{<:LinearAlgebra.UpperTriangular}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:755
convert(T::Type{<:LinearAlgebra.Diagonal}, m::SparseArrays.AbstractSparseMatrixCSC) in SparseArrays at /opt/homebrew/Cellar/julia/1.8.5/share/julia/stdlib/v1.8/SparseArrays/src/sparsematrix.jl:747
convert(::Type{Union{}}, a::AbstractArray) in Base at array.jl:618
convert(::Type{T}, M::AbstractArray) where T<:OffsetArrays.OffsetArray in OffsetArrays at /Users/greatsage/.julia/packages/OffsetArrays/TcCEq/src/OffsetArrays.jl:256
convert(::Type{T}, a::AbstractArray) where T<:Array in Base at array.jl:617
convert(::Type{SA}, a::AbstractArray) where SA<:StaticArraysCore.StaticArray in StaticArrays at /Users/greatsage/.julia/packages/StaticArrays/4uslg/src/convert.jl:194
convert(T::Type{<:BitArray}, a::AbstractArray) in Base at bitarray.jl:580
convert(::Type{Union{}}, x) in Base at essentials.jl:213
convert(::Type{T}, obj) where T<:FunctionWrappers.FunctionWrapper in FunctionWrappers at /Users/greatsage/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:113
convert(::Type{T}, arg) where T<:VecElement in Base at baseext.jl:19
Possible fix, define
convert(::Type{Union{}}, ::SparseArrays.AbstractSparseMatrixCSC)
Stacktrace:
[1] Sparspak.SpkSparseSolver.SparseSolver{Int64, Float64}(p::SparseArrays.SparseMatrixCSC{Float64, Int64}, slvr::Sparspak.SpkSparseBase._SparseBase{Int64, Float64}, n::Int64, ma::Int64, na::Int64, mc::Int64, nc::Int64, _inmatrixdone::Bool, _orderdone::Bool, _symbolicdone::Bool, _factordone::Bool, _trisolvedone::Bool, _refinedone::Bool, _condestdone::Bool) (repeats 2 times)
@ Sparspak.SpkSparseSolver ~/.julia/packages/Sparspak/oqBYl/src/SparseMethod/SpkSparseSolver.jl:18
[2] Sparspak.SpkSparseSolver.SparseSolver(m::SparseArrays.SparseMatrixCSC{Float64, Int64})
@ Sparspak.SparseCSCInterface ~/.julia/packages/Sparspak/oqBYl/src/SparseCSCInterface/SparseCSCInterface.jl:189
[3] sparspaklu(m::SparseArrays.SparseMatrixCSC{Float64, Int64}; factorize::Bool)
@ Sparspak.SparseCSCInterface ~/.julia/packages/Sparspak/oqBYl/src/SparseCSCInterface/SparseCSCInterface.jl:219
[4] init_cacheval(#unused#::LinearSolve.SparspakFactorization, A::SparseArrays.SparseMatrixCSC{Float64, Int64}, b::Vector{Float64}, u::Vector{Float64}, Pl::IterativeSolvers.Identity, Pr::IterativeSolvers.Identity, maxiters::Int64, abstol::Float64, reltol::Float64, verbose::Bool, assumptions::LinearSolve.OperatorAssumptions{Nothing})
@ LinearSolve ~/.julia/packages/LinearSolve/dxfUd/src/factorization.jl:514
[5] init(::SciMLBase.LinearProblem{Nothing, true, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}, SciMLBase.NullParameters, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, ::LinearSolve.SparspakFactorization; alias_A::Bool, alias_b::Bool, abstol::Float64, reltol::Float64, maxiters::Int64, verbose::Bool, Pl::IterativeSolvers.Identity, Pr::IterativeSolvers.Identity, assumptions::LinearSolve.OperatorAssumptions{Nothing}, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ LinearSolve ~/.julia/packages/LinearSolve/dxfUd/src/common.jl:117
[6] init(::SciMLBase.LinearProblem{Nothing, true, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}, SciMLBase.NullParameters, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, ::LinearSolve.SparspakFactorization)
@ LinearSolve ~/.julia/packages/LinearSolve/dxfUd/src/common.jl:88
[7] solve(::SciMLBase.LinearProblem{Nothing, true, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}, SciMLBase.NullParameters, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, ::LinearSolve.SparspakFactorization; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ LinearSolve ~/.julia/packages/LinearSolve/dxfUd/src/common.jl:157
[8] solve(::SciMLBase.LinearProblem{Nothing, true, SparseArrays.SparseMatrixCSC{Float64, Int64}, Vector{Float64}, SciMLBase.NullParameters, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}}, ::LinearSolve.SparspakFactorization)
@ LinearSolve ~/.julia/packages/LinearSolve/dxfUd/src/common.jl:154
[9] macro expansion
@ ~/.julia/packages/LinearSolve/dxfUd/src/LinearSolve.jl:92 [inlined]
[10] top-level scope
@ ~/.julia/packages/SnoopPrecompile/1XXT1/src/SnoopPrecompile.jl:62
[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::Nothing)
@ Base ./loading.jl:1554
[13] top-level scope
@ stdin:1
in expression starting at /Users/greatsage/.julia/packages/LinearSolve/dxfUd/src/LinearSolve.jl:1
in expression starting at stdin:1
ERROR: Failed to precompile LinearSolve [7ed4a6bd-45f5-4d41-b270-4a48e9bafcae] to /Users/greatsage/.julia/compiled/v1.8/LinearSolve/jl_WHRT78.
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

j-fu · 2023-04-17T08:28:55Z

Does not work for me. Homebrew Julia, some info:

Did you try on a non-homebrew Julia ? So far it seems that this is a subtle bug of the homebrew build.

Fedster · 2023-04-17T09:34:17Z

Does not work for me. Homebrew Julia, some info:

Did you try on a non-homebrew Julia ? So far it seems that this is a subtle bug of the homebrew build.

Sadly not due to time issues -- I was wondering whether I should try the cask and not the formula

Fedster · 2023-04-17T11:31:28Z

ok, I nuked the whole homebrew, reinstalled the official binary and no problem, so it is homebrew, which is annoying because I like automated update tracking with it.

oscardssmith · 2023-04-17T11:51:30Z

juliaup gives the automatic update tracking without providing broken versions of Julia.

ChrisRackauckas · 2023-04-17T12:00:18Z

Fixed the title. Indeed at this point it's not really a question of what the issue is anymore, it's been repeated dozens of times. Julia's Homebrew build doesn't evaluate Julia scripts exactly like the Julia programming language, and whatever language it is is not something this package is written for. Until it's updated to act like the Julia programming language, we highly recommend people install Julia from https://julialang.org/ or use juliaup https://github.com/JuliaLang/juliaup

philippemiron · 2023-04-19T05:24:02Z

As I said a few comments above, the brew cast already points to https://julialang-s3.julialang.org/bin/mac/#{arch}/#{version.major_minor}/julia-#{version}-mac#{arch.delete_prefix("x")}.dmg, which I guess is an official source (?).

The full installation is done by the following script:

cask "julia" do
  arch arm: "aarch64", intel: "x64"

  version "1.8.5"
  sha256 arm:   "7f6a23a4a1d864f69e65b1542fd3d1cf324d59c922ac43804b1ba077b9cc475d",
         intel: "22afd5e28a8a809dc7be0bc99cf491391a31af5669b173cf3318e433274148db"

  url "https://julialang-s3.julialang.org/bin/mac/#{arch}/#{version.major_minor}/julia-#{version}-mac#{arch.delete_prefix("x")}.dmg"
  name "Julia"
  desc "Programming language for technical computing"
  homepage "https://julialang.org/"

  livecheck do
    url "https://julialang.org/downloads/"
    regex(/href=.*?julia[._-]v?(\d+(?:\.\d+)+)[._-]mac#{arch.delete_prefix("x")}\.dmg/i)
  end

  app "Julia-#{version.major_minor}.app"
  binary "#{appdir}/Julia-#{version.major_minor}.app/Contents/Resources/julia/bin/julia"

  zap trash: [
    "~/.julia",
    "~/Library/Logs/Julia",
    "~/Library/Preferences/com.github.Julia.plist",
    "~/Library/Preferences/julia.plist",
    "~/Library/Saved Application State/com.github.Julia.savedState",
  ]
end

I think it would be better to add/modify those steps to properly install julia, instead of hoping for people to install it manually from the website.

Fedster · 2023-04-19T06:06:45Z

I removed the 'official' Julia, I then installed Juliaup with homebrew and everything still works, so my problem was somehow caused by the homebrew julia installation.

@philippemiron I see both a Julia formula ('brew install julia') and a Cask ('brew install --cask julia') in homebrew, and it is the julia installed by the formula that seems to be the problem.

philippemiron · 2023-04-19T06:13:06Z

Ok that makes more sense. The regular formula is performing many more steps during installation...

liiyung · 2023-06-13T13:05:36Z

Dropping by to say I also encountered this issue, on macOS and M1 chip.

Versions :
Monterey 12.6
brew --version 4.0.22
julia 1.9.0

I initially installed Julia with brew install julia. Having seen this thread, I removed the first install and reinstalled with brew install --cask julia and that seemed to solve the issue. Perhaps it might be good to mention somewhere that brew install julia still causes this issue?

YingboMa closed this as completed Feb 6, 2023

ChrisRackauckas reopened this Feb 6, 2023

j-fu mentioned this issue Feb 6, 2023

LinearSolve fails to precompile on julia 1.8.5 #266

Closed

mcasanova1445 mentioned this issue Feb 8, 2023

Precompiling fails on Julia 1.8.5 qojulia/QuantumOptics.jl#359

Closed

ChrisRackauckas mentioned this issue Feb 21, 2023

Precompilation problem (OrdinaryDiffEq v6.41.0) SciML/OrdinaryDiffEq.jl#1857

Closed

ChrisRackauckas mentioned this issue Mar 27, 2023

Precompilation fails when updating SciML/OrdinaryDiffEq.jl#1919

Closed

ChrisRackauckas changed the title ~~Package not Precompiling~~ Homebrew's Julia Build is not built correctly and causes package precompilation errors Apr 17, 2023

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Homebrew's Julia Build is not built correctly and causes package precompilation errors #271

Homebrew's Julia Build is not built correctly and causes package precompilation errors #271

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Homebrew's Julia Build is not built correctly and causes package precompilation errors #271

Homebrew's Julia Build is not built correctly and causes package precompilation errors #271

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