installation issue -- precompilation error

[rseydam]

Hey,

I currently installed the latest julia and BifucationKit.jl. When installing HclinicBifurcaitonKit.jl i get some complaint about compatibility:

⌅ [0f109fa4] BifurcationKit v0.3.6
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use status --outdated
⌅ [0f109fa4] BifurcationKit v0.3.6 (<v0.4.4): HclinicBifurcationKit

Installation of the HclinicBifurcationKit.jl gives the following error and i don't know how i can fix this

Precompiling project...
✗ BifurcationKit
✗ HclinicBifurcationKit
0 dependencies successfully precompiled in 9 seconds. 298 already precompiled.

ERROR: The following 2 direct dependencies failed to precompile:

BifurcationKit

Failed to precompile BifurcationKit [0f109fa4-8a5d-4b75-95aa-f515264e7665] to "C:\Users\RichardEydam\.julia\compiled\v1.11\BifurcationKit\jl_B690.tmp".
ERROR: LoadError: ArgumentError: invalid type for argument A in method definition for rmul! at C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BorderedArrays.jl:69
Stacktrace:
[1] top-level scope
@ C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BorderedArrays.jl:69
[2] include(mod::Module, _path::String)
@ Base .\Base.jl:557
[3] include(x::String)
@ BifurcationKit C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BifurcationKit.jl:1
[4] top-level scope
@ C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BifurcationKit.jl:24
[5] include
@ .\Base.jl:557 [inlined]
[6] 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:2790
[7] top-level scope
@ stdin:5
in expression starting at C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BorderedArrays.jl:69
in expression starting at C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BifurcationKit.jl:1
in expression starting at stdin:5
HclinicBifurcationKit

Failed to precompile HclinicBifurcationKit [0e751702-a6d5-4e4e-bf0f-194619fbec56] to "C:\Users\RichardEydam\.julia\compiled\v1.11\HclinicBifurcationKit\jl_C307.tmp".
ERROR: LoadError: ArgumentError: invalid type for argument A in method definition for rmul! at C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BorderedArrays.jl:69
Stacktrace:
[1] top-level scope
@ C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BorderedArrays.jl:69
[2] include(mod::Module, _path::String)
@ Base .\Base.jl:557
[3] include(x::String)
@ BifurcationKit C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BifurcationKit.jl:1
[4] top-level scope
@ C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BifurcationKit.jl:24
[5] include
@ .\Base.jl:557 [inlined]
[6] 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::String)
@ Base .\loading.jl:2790
[7] top-level scope
@ stdin:5
in expression starting at C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BorderedArrays.jl:69
in expression starting at C:\Users\RichardEydam.julia\packages\BifurcationKit\2LYxR\src\BifurcationKit.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile BifurcationKit [0f109fa4-8a5d-4b75-95aa-f515264e7665] to "C:\Users\RichardEydam\.julia\compiled\v1.11\BifurcationKit\jl_C440.tmp".
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; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, isext::Bool)
@ Base .\loading.jl:3085
[3] (::Base.var"#1082#1083"{Base.PkgId})()
@ Base .\loading.jl:2492
[4] mkpidlock(f::Base.var"#1082#1083"{Base.PkgId}, at::String, pid::Int32; kwopts::@kwargs{stale_age::Int64, wait::Bool})
@ FileWatching.Pidfile C:\Users\RichardEydam.julia\juliaup\julia-1.11.1+0.x64.w64.mingw32\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:95
[5] #mkpidlock#6
@ C:\Users\RichardEydam.julia\juliaup\julia-1.11.1+0.x64.w64.mingw32\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:90 [inlined]
[6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@kwargs{stale_age::Int64})
@ FileWatching.Pidfile C:\Users\RichardEydam.julia\juliaup\julia-1.11.1+0.x64.w64.mingw32\share\julia\stdlib\v1.11\FileWatching\src\pidfile.jl:116
[7] #invokelatest#2
@ .\essentials.jl:1057 [inlined]
[8] invokelatest
@ .\essentials.jl:1052 [inlined]
[9] maybe_cachefile_lock(f::Base.var"#1082#1083"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
@ Base .\loading.jl:3609
[10] maybe_cachefile_lock
@ .\loading.jl:3606 [inlined]
[11] _require(pkg::Base.PkgId, env::String)
@ Base .\loading.jl:2488
[12] __require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base .\loading.jl:2315
[13] #invoke_in_world#3
@ .\essentials.jl:1089 [inlined]
[14] invoke_in_world
@ .\essentials.jl:1086 [inlined]
[15] _require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base .\loading.jl:2302
[16] macro expansion
@ .\loading.jl:2241 [inlined]
[17] macro expansion
@ .\lock.jl:273 [inlined]
[18] __require(into::Module, mod::Symbol)
@ Base .\loading.jl:2198
[19] #invoke_in_world#3
@ .\essentials.jl:1089 [inlined]
[20] invoke_in_world
@ .\essentials.jl:1086 [inlined]
[21] require(into::Module, mod::Symbol)
@ Base .\loading.jl:2191
[22] include
@ .\Base.jl:557 [inlined]
[23] 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:2790
[24] top-level scope
@ stdin:5
in expression starting at C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\HclinicBifurcationKit.jl:1
in expression starting at stdin:5

[rveltz]

Hi,

That is because https://github.com/bifurcationkit/HclinicBifurcationKit.jl/blob/main/Project.toml#L17. Can you try to update this and see if it works?

[rseydam]

I am not entirely sure if I understand correctly. I change the line to

BifurcationKit = "^0.3.6, ^0.4.4"

I then updated BifurcationKit again to 0.4.4 and tried to install HclinicBifurcationKit, though it still reverted BifurcationKit to v0.3.6 and failed to precompile. Am I missing a step here?

[rveltz]

you probably need:

] resolve

[rseydam]

I installed BifurcationKit v0.4.4 and changed in the compat to

BifurcationKit = "^0.4.4"

Now it still has errors in precompilation with v0.4.4.

Precompiling HclinicBifurcationKit...
Info Given HclinicBifurcationKit was explicitly requested, output will be shown live
ERROR: LoadError: UndefVarError: @set not defined in HclinicBifurcationKit
Stacktrace:
[1] top-level scope
@ :0
[2] include(mod::Module, _path::String)
@ Base .\Base.jl:557
[3] include(x::String)
@ HclinicBifurcationKit C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\HclinicBifurcationKit.jl:1
[4] top-level scope
@ C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\HclinicBifurcationKit.jl:15
[5] include
@ .\Base.jl:557 [inlined]
[6] 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:2790
[7] top-level scope
@ stdin:5
in expression starting at C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\StandardShooting.jl:72
in expression starting at C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\StandardShooting.jl:68
in expression starting at C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\HclinicBifurcationKit.jl:1
in expression starting at stdin:5
✗ HclinicBifurcationKit
0 dependencies successfully precompiled in 6 seconds. 273 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

HclinicBifurcationKit

Failed to precompile HclinicBifurcationKit [0e751702-a6d5-4e4e-bf0f-194619fbec56] to "C:\Users\RichardEydam\.julia\compiled\v1.11\HclinicBifurcationKit\jl_671C.tmp".
ERROR: LoadError: UndefVarError: @set not defined in HclinicBifurcationKit
Stacktrace:
[1] top-level scope
@ :0
[2] include(mod::Module, _path::String)
@ Base .\Base.jl:557
[3] include(x::String)
@ HclinicBifurcationKit C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\HclinicBifurcationKit.jl:1
[4] top-level scope
@ C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\HclinicBifurcationKit.jl:15
[5] include
@ .\Base.jl:557 [inlined]
[6] 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:2790
[7] top-level scope
@ stdin:5
in expression starting at C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\StandardShooting.jl:72
in expression starting at C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\StandardShooting.jl:68
in expression starting at C:\Users\RichardEydam.julia\packages\HclinicBifurcationKit\hOVPL\src\HclinicBifurcationKit.jl:1
in expression starting at stdin:

[rveltz]

That's because it is not exported by BK. Try BifurcationKit.@set

[rseydam]

I added BifurcationKit.@set in StandardShooting.jl, and then I could build the package but running it still leads to some issues. It complained about the ambiguity of set in HomProblemPBC.jl in particular. I was unsure which ones should call BK.set and which should call Setfield.set. So first I changed them all to BK.set. Now I tried to run the example freire from the docs and after a few changes to the code (some things in it might be dated) I run into this problem

────────────────────────────
┌─ Start Hom_BT init
├─ ϵ = 0.018431210680221747
├─── ζ = 0.07071067811865475
ERROR: MethodError: no method matching newton(::BifurcationProblem{…}, ::NewtonPar{…})
The function newton exists, but no method is defined for this combination of argument types.

Closest candidates are:
newton(::BifurcationKit.AbstractBifurcationProblem, ::vectype, ::vectype, ::Any, ::NewtonPar{T, L, E}; ...) where {T, vectype, L, E}
@ BifurcationKit C:\Users\RichardEydam.julia\packages\BifurcationKit\RaJtn\src\DeflationOperator.jl:361
newton(::BifurcationKit.AbstractBifurcationProblem, ::vectype, ::vectype, ::Any, ::NewtonPar{T, L, E}, ::DeflationOperator; ...) where {T, vectype
@ BifurcationKit C:\Users\RichardEydam.julia\packages\BifurcationKit\RaJtn\src\DeflationOperator.jl:361
newton(::BifurcationKit.AbstractBifurcationProblem, ::vectype, ::vectype, ::Any, ::NewtonPar{T, L, E}, ::DeflationOperator, ::Any; kwargs...) wher
@ BifurcationKit C:\Users\RichardEydam.julia\packages\BifurcationKit\RaJtn\src\DeflationOperator.jl:361
...

Stacktrace:
[1] continuation(prob_vf::BifurcationProblem{…}, bt::BifurcationKit.BogdanovTakens{…}, bvp::PeriodicOrbitOCollProblem{…}, alg::PALC{…}, _contParams64, freeparams::Tuple{…}, maxT::Float64, update_every_step::Int64, test_orbit_flip::Bool, test_inclination_flip::Bool, kwargs::@kwargs{…})
@ HclinicBifurcationKit C:\Users\RichardEydam.julia\dev\HclinicBifurcationKit\src\HomProblemPBC.jl:413
[2] top-level scope
@ Untitled-1:66

[rveltz]

That's because the new syntax is solve(prob, Newton(), optn)

[GabrieleCasagrande]

Hi,
sorry to interrupt the discussion but I'm also interested in using HclinicBifurcationKit.jl.
I tried to follow your suggestions and I was also able to precompile the package, however when I try to test it with Pkg.test() I receive the following error message

Testing Running tests...
HclinicBifurcationKit.jl: Error During Test at /home/gabricasa/HclinicBifurcationKit.jl/test/runtests.jl:4
Got exception outside of a @test
LoadError: AssertionError: lens isa Int || lens isa AllOpticTypes
Stacktrace:
[1] BifurcationProblem(_F::typeof(Fbt), u0::Vector{Float64}, parms::@NamedTuple{β1::Float64, β2::Float64, a::Float64, b::Float64}, lens::Setfield.PropertyLens{:β1}; jvp::Nothing, vjp::Nothing, J::Nothing, J!::Nothing, Jᵗ::Nothing, d2F::Nothing, d3F::Nothing, issymmetric::Bool, record_from_solution::typeof(BifurcationKit.record_sol_default), plot_solution::typeof(BifurcationKit.plot_default), delta::Float64, save_solution::typeof(BifurcationKit.save_solution_default), inplace::Bool)
@ BifurcationKit ~/.julia/packages/BifurcationKit/RaJtn/src/Problems.jl:221
[2] BifurcationProblem(_F::Function, u0::Vector{Float64}, parms::@NamedTuple{β1::Float64, β2::Float64, a::Float64, b::Float64}, lens::Setfield.PropertyLens{:β1})
@ BifurcationKit ~/.julia/packages/BifurcationKit/RaJtn/src/Problems.jl:207
[3] top-level scope
@ ~/HclinicBifurcationKit.jl/test/testHomoclinic.jl:16
[4] include(fname::String)
@ Main ./sysimg.jl:38
[5] macro expansion
@ ~/HclinicBifurcationKit.jl/test/runtests.jl:5 [inlined]
[6] macro expansion
@ ~/.julia/juliaup/julia-1.11.1+0.x64.linux.gnu/share/julia/stdlib/v1.11/Test/src/Test.jl:1700 [inlined]
[7] top-level scope
@ ~/HclinicBifurcationKit.jl/test/runtests.jl:5
[8] include(fname::String)
@ Main ./sysimg.jl:38
[9] top-level scope
@ none:6
[10] eval
@ ./boot.jl:430 [inlined]
[11] exec_options(opts::Base.JLOptions)
@ Base ./client.jl:296
[12] _start()
@ Base ./client.jl:531
in expression starting at /home/gabricasa/HclinicBifurcationKit.jl/test/testHomoclinic.jl:16
Test Summary: | Error Total Time
HclinicBifurcationKit.jl | 1 1 1.7s
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /home/gabricasa/HclinicBifurcationKit.jl/test/runtests.jl:4
ERROR: Package HclinicBifurcationKit errored during testing
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types ~/.julia/juliaup/julia-1.11.1+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68
[2] test(ctx::Pkg.Types.Context, pkgs::Vector{…}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.1+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2104
[3] test
@ ~/.julia/juliaup/julia-1.11.1+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1989 [inlined]
[4] test(ctx::Pkg.Types.Context, pkgs::Vector{…}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@kwargs{…})
@ Pkg.API ~/.julia/juliaup/julia-1.11.1+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:475
[5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@kwargs{})
@ Pkg.API ~/.julia/juliaup/julia-1.11.1+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
[6] test(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API ~/.julia/juliaup/julia-1.11.1+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:148
[7] test(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::Nothing, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::@kwargs{})
@ Pkg.API ~/.julia/juliaup/julia-1.11.1+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:174
[8] test()
@ Pkg.API ~/.julia/juliaup/julia-1.11.1+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:165
[9] top-level scope
@ REPL[38]:1

[rveltz]

OK ill correct it asap

[rveltz]

it should be corrected on master. Ill push a tag soon