Getting issue in chain_sde while doing MCMC inference solution for SDEs

Virendra_Sheoran · October 14, 2022, 7:50am

(@v1.8) pkg> update
Updating registry at C:\Users\User\.julia\registries\General.toml
Updating git-repo https://github.com/TuringLang/TuringTutorials
No Changes to C:\Users\User\.julia\environments\v1.8\Project.toml
No Changes to C:\Users\User\.julia\environments\v1.8\Manifest.toml

(@v1.8) pkg> build DifferentialEquations

(@v1.8) pkg> build Sundials

(@v1.8) pkg> BinaryProvider
ERROR: BinaryProvider is not a recognized command. Type ? for help with available commands

(@v1.8) pkg> build BinaryProvider

(@v1.8) pkg>

i am getting nothing from all these builds.

but when i run the following code

using Turing
using DifferentialEquations
using OrdinaryDiffEq, DiffEqParamEstim, JuMP, NLopt, Plots

Load StatsPlots for visualizations and diagnostics.

using StatsPlots

using LinearAlgebra
using DiffEqParamEstim
using DiffEqBayes
using Optim

Set a seed for reproducibility.

using Random
Random.seed!(14);

i get following error

ERROR: LoadError: InitError: could not load library “C:\Users\User.julia\artifacts\4ccc575631c856942ae91cbb8294de9b0a746c9d\bin\libsundials_sunnonlinsolfixedpoint.dll”
The specified module could not be found.
Stacktrace:
[1] dlopen(s::String, flags::UInt32; throw_error::Bool)
@ Base.Libc.Libdl .\libdl.jl:117
[2] dlopen(s::String, flags::UInt32)
@ Base.Libc.Libdl .\libdl.jl:116
[3] macro expansion
@ C:\Users\User.julia\packages\JLLWrappers\QpMQW\src\products\library_generators.jl:54 [inlined]
[4] init()
@ Sundials_jll C:\Users\User.julia\packages\Sundials_jll\rXn1i\src\wrappers\x86_64-w64-mingw32-libgfortran5.jl:159
[5] _include_from_serialized(pkg::Base.PkgId, path::String, depmods::Vector{Any})
@ Base .\loading.jl:831
[6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt64)
@ Base .\loading.jl:1039
[7] _require(pkg::Base.PkgId)
@ Base .\loading.jl:1315
[8] _require_prelocked(uuidkey::Base.PkgId)
@ Base .\loading.jl:1200
[9] macro expansion
@ .\loading.jl:1180 [inlined]
[10] macro expansion
@ .\lock.jl:223 [inlined]
[11] require(into::Module, mod::Symbol)
@ Base .\loading.jl:1144
[12] include
@ .\Base.jl:419 [inlined]
[13] 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:1554
[14] top-level scope
@ stdin:1
during initialization of module Sundials_jll
in expression starting at C:\Users\User.julia\packages\Sundials\3c9Un\src\Sundials.jl:3
in expression starting at stdin:1
ERROR: LoadError: Failed to precompile Sundials [c3572dad-4567-51f8-b174-8c6c989267f4] to C:\Users\User.julia\compiled\v1.8\Sundials\jl_A525.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)
@ 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
[9] include
@ .\Base.jl:419 [inlined]
[10] 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
[11] top-level scope
@ stdin:1
in expression starting at C:\Users\User.julia\packages\DifferentialEquations\el96s\src\DifferentialEquations.jl:1
in expression starting at stdin:1
Failed to precompile DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa] to C:\Users\User.julia\compiled\v1.8\DifferentialEquations\jl_883E.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)
@ 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
[9] eval
@ .\boot.jl:368 [inlined]
[10] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
@ Base .\loading.jl:1428

ChrisRackauckas · October 14, 2022, 10:28am

Try deleting that folder and then reinstalling your packages. Something about your package folder seems corrupted. It’s like you lost internet while it was downloading a file, and it’s having trouble recovering.

Virendra_Sheoran · October 14, 2022, 11:19am

(@v1.8) pkg> add DiffEqBayes
Resolving package versions…
ERROR: Unsatisfiable requirements detected for package Turing [fce5fe82]:
Turing [fce5fe82] log:
├─possible versions are: 0.5.0-0.21.12 or uninstalled
├─restricted by compatibility requirements with DiffEqBayes [ebbdde9d] to versions: 0.5.0-0.16.6
│ └─DiffEqBayes [ebbdde9d] log:
│ ├─possible versions are: 0.8.0-3.1.0 or uninstalled
│ ├─restricted to versions * by an explicit requirement, leaving only versions 0.8.0-3.1.0
│ ├─restricted by compatibility requirements with Distributions [31c24e10] to versions: 0.8.0-2.26.0 or uninstalled, leaving only versions: 0.8.0-2.26.0
│ │ └─Distributions [31c24e10] log:
│ │ ├─possible versions are: 0.16.0-0.25.76 or uninstalled
│ │ ├─restricted to versions * by an explicit requirement, leaving only versions 0.16.0-0.25.76
│ │ ├─restricted by compatibility requirements with Bridge [2d3116d5] to versions: 0.16.0-0.24.18
│ │ │ └─Bridge [2d3116d5] log:
│ │ │ ├─possible versions are: 0.9.0-0.11.6 or uninstalled
│ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions 0.9.0-0.11.6
│ │ │ ├─restricted by compatibility requirements with Distributions [31c24e10] to versions: 0.11.1-0.11.6 or uninstalled, leaving only versions: 0.11.1-0.11.6
│ │ │ │ └─Distributions [31c24e10] log: see above
│ │ │ ├─restricted by compatibility requirements with RecipesBase [3cdcf5f2] to versions: 0.11.2-0.11.6 or uninstalled, leaving only versions: 0.11.2-0.11.6
│ │ │ │ └─RecipesBase [3cdcf5f2] log:
│ │ │ │ ├─possible versions are: 0.4.0-1.3.0 or uninstalled
│ │ │ │ ├─restricted by compatibility requirements with StatsPlots [f3b207a7] to versions: 0.5.0-1.3.0
│ │ │ │ │ └─StatsPlots [f3b207a7] log:
│ │ │ │ │ ├─possible versions are: 0.10.0-0.15.4 or uninstalled
│ │ │ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions 0.10.0-0.15.4
│ │ │ │ │ └─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 0.14.4-0.15.4 or uninstalled, leaving only versions: 0.14.4-0.15.4
│ │ │ │ │ └─Plots [91a5bcdd] log:
│ │ │ │ │ ├─possible versions are: 0.12.1-1.35.3 or uninstalled
│ │ │ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions 0.12.1-1.35.3
│ │ │ │ │ ├─restricted by compatibility requirements with StatsPlots [f3b207a7] to versions: 0.14.0-1.35.3
│ │ │ │ │ │ └─StatsPlots [f3b207a7] log: see above
│ │ │ │ │ └─restricted by compatibility requirements with SciMLTutorials [30cb0354] to versions: 1.6.0-1.35.3
│ │ │ │ │ └─SciMLTutorials [30cb0354] log:
│ │ │ │ │ ├─possible versions are: 0.8.0-1.0.0 or uninstalled
│ │ │ │ │ └─restricted to versions * by an explicit requirement, leaving only versions 0.8.0-1.0.0
│ │ │ │ └─restricted by compatibility requirements with Plots [91a5bcdd] to versions: 1.0.0-1.3.0
│ │ │ │ └─Plots [91a5bcdd] log: see above
│ │ │ └─restricted by compatibility requirements with SpecialFunctions [276daf66] to versions: [0.9.0-0.11.4, 0.11.6] or uninstalled, leaving only versions: [0.11.2-0.11.4, 0.11.6]
│ │ │ └─SpecialFunctions [276daf66] log:
│ │ │ ├─possible versions are: 0.7.0-2.1.7 or uninstalled
│ │ │ ├─restricted by compatibility requirements with Distributions [31c24e10] to versions: 0.7.0-1.8.7
│ │ │ │ └─Distributions [31c24e10] log: see above
│ │ │ ├─restricted by compatibility requirements with Turing [fce5fe82] to versions: 0.7.2-1.8.7
│ │ │ │ └─Turing [fce5fe82] log: see above
│ │ │ ├─restricted by compatibility requirements with Distributions [31c24e10] to versions: 0.8.0-1.8.7
│ │ │ │ └─Distributions [31c24e10] log: see above
│ │ │ └─restricted by compatibility requirements with CUDA [052768ef] to versions: 1.3.0-2.1.7, leaving only versions: 1.3.0-1.8.7
│ │ │ └─CUDA [052768ef] log:
│ │ │ ├─possible versions are: 0.1.0-3.12.0 or uninstalled
│ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions 0.1.0-3.12.0
│ │ │ ├─restricted by julia compatibility requirements to versions: [2.3.0, 2.5.0-3.12.0] or uninstalled, leaving only versions: [2.3.0, 2.5.0-3.12.0]
│ │ │ └─restricted by compatibility requirements with LLVM [929cbde3] to versions: 3.3.3-3.12.0 or uninstalled, leaving only versions: 3.3.3-3.12.0
│ │ │ └─LLVM [929cbde3] log:
│ │ │ ├─possible versions are: 0.9.0-4.14.0 or uninstalled
│ │ │ ├─restricted by julia compatibility requirements to versions: 4.0.0-4.14.0 or uninstalled
│ │ │ └─restricted by compatibility requirements with CUDA [052768ef] to versions: 3.0.0-4.14.0, leaving only versions: 4.0.0-4.14.0
│ │ │ └─CUDA [052768ef] log: see above
│ │ ├─restricted by compatibility requirements with StatsBase [2913bbd2] to versions: 0.21.1-0.25.76 or uninstalled, leaving only versions: 0.21.1-0.24.18
│ │ │ └─StatsBase [2913bbd2] log:
│ │ │ ├─possible versions are: 0.24.0-0.33.21 or uninstalled
│ │ │ ├─restricted by compatibility requirements with IPMeasures [d7dc6e0c] to versions: 0.32.0-0.33.21
│ │ │ │ └─IPMeasures [d7dc6e0c] log:
│ │ │ │ ├─possible versions are: 0.1.0-0.2.4 or uninstalled
│ │ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions 0.1.0-0.2.4
│ │ │ │ ├─restricted by compatibility requirements with CUDA [052768ef] to versions: [0.1.0-0.1.4, 0.2.2-0.2.4] or uninstalled, leaving only versions: [0.1.0-0.1.4, 0.2.2-0.2.4]
│ │ │ │ │ └─CUDA [052768ef] log: see above
│ │ │ │ ├─restricted by compatibility requirements with CuArrays [3a865a2d] to versions: [0.1.0-0.1.1, 0.2.0-0.2.4] or uninstalled, leaving only versions: [0.1.0-0.1.1, 0.2.2-0.2.4]
│ │ │ │ │ └─CuArrays [3a865a2d] log:
│ │ │ │ │ ├─possible versions are: 0.2.1-2.2.2 or uninstalled
│ │ │ │ │ └─restricted by julia compatibility requirements to versions: uninstalled
│ │ │ │ ├─restricted by compatibility requirements with Flux [587475ba] to versions: 0.1.2-0.2.4 or uninstalled, leaving only versions: 0.2.2-0.2.4
│ │ │ │ │ └─Flux [587475ba] log:
│ │ │ │ │ ├─possible versions are: 0.4.1-0.13.6 or uninstalled
│ │ │ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions 0.4.1-0.13.6
│ │ │ │ │ ├─restricted by compatibility requirements with CUDA [052768ef] to versions: [0.4.1-0.10.4, 0.11.2-0.13.6] or uninstalled, leaving only versions: [0.4.1-0.10.4, 0.11.2-0.13.6]
│ │ │ │ │ │ └─CUDA [052768ef] log: see above
│ │ │ │ │ ├─restricted by compatibility requirements with CuArrays [3a865a2d] to versions: [0.4.1-0.8.3, 0.11.0-0.13.6] or uninstalled, leaving only versions: [0.4.1-0.8.3, 0.11.2-0.13.6]
│ │ │ │ │ │ └─CuArrays [3a865a2d] log: see above
│ │ │ │ │ ├─restricted by compatibility requirements with Adapt [79e6a3ab] to versions: 0.11.0-0.13.6 or uninstalled, leaving only versions: 0.11.2-0.13.6
│ │ │ │ │ │ └─Adapt [79e6a3ab] log:
│ │ │ │ │ │ ├─possible versions are: 0.3.0-3.4.0 or uninstalled
│ │ │ │ │ │ ├─restricted by compatibility requirements with CUDA [052768ef] to versions: 2.2.0-3.4.0
│ │ │ │ │ │ │ └─CUDA [052768ef] log: see above
│ │ │ │ │ │ └─restricted by compatibility requirements with CUDA [052768ef] to versions: 3.3.0-3.4.0
│ │ │ │ │ │ └─CUDA [052768ef] log: see above
│ │ │ │ │ └─restricted by compatibility requirements with CUDA [052768ef] to versions: [0.4.1-0.10.4, 0.12.2-0.13.6] or uninstalled, leaving only versions: 0.12.2-0.13.6
│ │ │ │ │ └─CUDA [052768ef] log: see above
│ │ │ │ └─restricted by compatibility requirements with CUDA [052768ef] to versions: [0.1.0-0.1.4, 0.2.4] or uninstalled, leaving only versions: 0.2.4
│ │ │ │ └─CUDA [052768ef] log: see above
│ │ │ └─restricted by compatibility requirements with Flux [587475ba] to versions: 0.33.0-0.33.21
│ │ │ └─Flux [587475ba] log: see above
│ │ ├─restricted by compatibility requirements with Bijectors [76274a88] to versions: [0.16.0-0.22.6, 0.23.3-0.25.76], leaving only versions: [0.21.1-0.22.6, 0.23.3-0.24.18]
│ │ │ └─Bijectors [76274a88] log:
│ │ │ ├─possible versions are: 0.1.0-0.10.6 or uninstalled
│ │ │ ├─restricted by compatibility requirements with Turing [fce5fe82] to versions: [0.1.0-0.5.2, 0.6.4-0.9.11]
│ │ │ │ └─Turing [fce5fe82] log: see above
│ │ │ ├─restricted by compatibility requirements with Requires [ae029012] to versions: [0.1.0, 0.3.0-0.10.6] or uninstalled, leaving only versions: [0.1.0, 0.3.0-0.5.2, 0.6.4-0.9.11]
│ │ │ │ └─Requires [ae029012] log:
│ │ │ │ ├─possible versions are: 0.5.0-1.3.0 or uninstalled
│ │ │ │ └─restricted by compatibility requirements with Weave [44d3d7a6] to versions: 1.0.0-1.3.0
│ │ │ │ └─Weave [44d3d7a6] log:
│ │ │ │ ├─possible versions are: 0.6.0-0.10.10 or uninstalled
│ │ │ │ └─restricted by compatibility requirements with SciMLTutorials [30cb0354] to versions: 0.9.0-0.10.10
│ │ │ │ └─SciMLTutorials [30cb0354] log: see above
│ │ │ ├─restricted by compatibility requirements with NNlib [872c559c] to versions: [0.1.0-0.5.2, 0.8.1-0.10.6] or uninstalled, leaving only versions: [0.1.0, 0.3.0-0.5.2, 0.8.1-0.9.11]
│ │ │ │ └─NNlib [872c559c] log:
│ │ │ │ ├─possible versions are: 0.3.2-0.8.9 or uninstalled
│ │ │ │ ├─restricted by compatibility requirements with LoopVectorization [bdcacae8] to versions: [0.3.2-0.7.1, 0.7.4-0.8.9] or uninstalled, leaving only versions: [0.3.2-0.7.1, 0.7.4-0.8.9]
│ │ │ │ │ └─LoopVectorization [bdcacae8] log:
│ │ │ │ │ ├─possible versions are: 0.1.0-0.12.133 or uninstalled
│ │ │ │ │ ├─restricted by julia compatibility requirements to versions: 0.9.0-0.12.133 or uninstalled
│ │ │ │ │ └─restricted by compatibility requirements with VectorizationBase [3d5dd08c] to versions: 0.12.19-0.12.133 or uninstalled
│ │ │ │ │ └─VectorizationBase [3d5dd08c] log:
│ │ │ │ │ ├─possible versions are: 0.1.0-0.21.51 or uninstalled
│ │ │ │ │ └─restricted by julia compatibility requirements to versions: 0.20.8-0.21.51 or uninstalled
│ │ │ │ ├─restricted by compatibility requirements with Requires [ae029012] to versions: 0.6.0-0.8.9 or uninstalled, leaving only versions: [0.6.0-0.7.1, 0.7.4-0.8.9]
│ │ │ │ │ └─Requires [ae029012] log: see above
│ │ │ │ ├─restricted by compatibility requirements with Flux [587475ba] to versions: 0.7.0-0.8.9, leaving only versions: [0.7.0-0.7.1, 0.7.4-0.8.9]
│ │ │ │ │ └─Flux [587475ba] log: see above
│ │ │ │ └─restricted by compatibility requirements with Flux [587475ba] to versions: 0.7.14-0.8.9
│ │ │ │ └─Flux [587475ba] log: see above
│ │ │ └─restricted by compatibility requirements with Turing [fce5fe82] to versions: 0.8.0-0.9.11, leaving only versions: 0.8.1-0.9.11
│ │ │ └─Turing [fce5fe82] log: see above
│ │ ├─restricted by compatibility requirements with StatsBase [2913bbd2] to versions: 0.23.2-0.25.76 or uninstalled, leaving only versions: 0.23.3-0.24.18
│ │ │ └─StatsBase [2913bbd2] log: see above
│ │ └─restricted by compatibility requirements with SpecialFunctions [276daf66] to versions: 0.24.4-0.25.76 or uninstalled, leaving only versions: 0.24.4-0.24.18
│ │ └─SpecialFunctions [276daf66] log: see above
│ ├─restricted by compatibility requirements with Requires [ae029012] to versions: [0.8.0-1.3.0, 2.3.0-3.1.0] or uninstalled, leaving only versions: [0.8.0-1.3.0, 2.3.0-2.26.0]
│ │ └─Requires [ae029012] log: see above
│ ├─restricted by compatibility requirements with LogDensityProblems [6fdf6af0] to versions: [0.8.0-2.1.1, 2.9.0-2.26.0] or uninstalled, leaving only versions: [0.8.0-1.3.0, 2.9.0-2.26.0]
│ │ └─LogDensityProblems [6fdf6af0] log:
│ │ ├─possible versions are: 0.2.0-1.0.2 or uninstalled
│ │ ├─restricted by compatibility requirements with DiffEqBayes [ebbdde9d] to versions: 0.2.0-0.10.6
│ │ │ └─DiffEqBayes [ebbdde9d] log: see above
│ │ ├─restricted by compatibility requirements with Requires [ae029012] to versions: [0.2.0-0.4.0, 0.10.1-1.0.2] or uninstalled, leaving only versions: [0.2.0-0.4.0, 0.10.1-0.10.6]
│ │ │ └─Requires [ae029012] log: see above
│ │ └─restricted by compatibility requirements with Flux [587475ba] to versions: [0.2.0, 0.4.1-1.0.2] or uninstalled, leaving only versions: [0.2.0, 0.10.1-0.10.6]
│ │ └─Flux [587475ba] log: see above
│ └─restricted by compatibility requirements with Turing [fce5fe82] to versions: 2.17.0-2.26.0 or uninstalled, leaving only versions: 2.17.0-2.26.0
│ └─Turing [fce5fe82] log: see above
├─restricted by compatibility requirements with MCMCChain [1671dc4f] to versions: 0.6.11-0.21.12 or uninstalled, leaving only versions: 0.6.11-0.16.6
│ └─MCMCChain [1671dc4f] log:
│ ├─possible versions are: 0.1.0-0.2.3 or uninstalled
│ └─restricted by julia compatibility requirements to versions: uninstalled
├─restricted by compatibility requirements with Requires [ae029012] to versions: 0.8.0-0.21.12 or uninstalled, leaving only versions: 0.8.0-0.16.6
│ └─Requires [ae029012] log: see above
├─restricted by compatibility requirements with Bijectors [76274a88] to versions: [0.5.0-0.9.0, 0.9.2, 0.14.0-0.21.12] or uninstalled, leaving only versions: [0.8.0-0.9.0, 0.9.2, 0.14.0-0.16.6]
│ └─Bijectors [76274a88] log: see above
├─restricted by compatibility requirements with DiffEqBayes [ebbdde9d] to versions: [0.5.0-0.7.4, 0.9.0-0.16.6], leaving only versions: [0.9.0, 0.9.2, 0.14.0-0.16.6]
│ └─DiffEqBayes [ebbdde9d] log: see above
├─restricted by compatibility requirements with StatsBase [2913bbd2] to versions: [0.5.0-0.8.3, 0.11.0-0.21.12] or uninstalled, leaving only versions: 0.14.0-0.16.6
│ └─StatsBase [2913bbd2] log: see above
├─restricted by compatibility requirements with AdvancedPS [576499cb] to versions: 0.5.0-0.15.1 or uninstalled, leaving only versions: 0.14.0-0.15.1
│ └─AdvancedPS [576499cb] log:
│ ├─possible versions are: 0.1.0-0.4.0 or uninstalled
│ └─restricted by compatibility requirements with Libtask [6f1fad26] to versions: uninstalled
│ └─Libtask [6f1fad26] log:
│ ├─possible versions are: 0.1.1-0.8.2 or uninstalled
│ ├─restricted by compatibility requirements with Libtask_jll [3ae2931a] to versions: [0.1.1-0.4.2, 0.6.0-0.8.2] or uninstalled
│ │ └─Libtask_jll [3ae2931a] log:
│ │ ├─possible versions are: 0.3.0-0.5.1 or uninstalled
│ │ └─restricted by julia compatibility requirements to versions: [0.3.0-0.3.2, 0.5.0-0.5.1] or uninstalled
│ ├─restricted by compatibility requirements with Turing [fce5fe82] to versions: 0.1.1-0.5.3, leaving only versions: 0.1.1-0.4.2
│ │ └─Turing [fce5fe82] log: see above
│ └─restricted by compatibility requirements with Turing [fce5fe82] to versions: 0.4.0-0.5.3, leaving only versions: 0.4.0-0.4.2
│ └─Turing [fce5fe82] log: see above
└─restricted by compatibility requirements with SpecialFunctions [276daf66] to versions: [0.5.0-0.5.1, 0.15.4-0.21.12] or uninstalled — no versions left
└─SpecialFunctions [276daf66] log: see above

nilshg · October 14, 2022, 11:39am

This was covered before - please install the packages you need in a fresh environment to isolate the issue you’re facing.

ChrisRackauckas · October 14, 2022, 11:46am

This was deprecated years ago. Something is very wrong with your installation. There’s a lot of junk. You should really just start from scratch.

Virendra_Sheoran · October 14, 2022, 11:49am

yes i have unisnstalled everything now, downloading latest version of julia from following link

fist i will install latest julia and then install required packages one by one

Virendra_Sheoran · October 14, 2022, 1:46pm

following is my st-m

(@v1.8) pkg> st -m
Status C:\Users\viren\.julia\environments\v1.8\Manifest.toml
⌅ [c3fe647b] AbstractAlgebra v0.15.1
⌃ [621f4979] AbstractFFTs v1.0.1
⌅ [80f14c24] AbstractMCMC v1.0.1
⌅ [1520ce14] AbstractTrees v0.3.4
[79e6a3ab] Adapt v3.4.0
⌅ [0bf59076] AdvancedHMC v0.2.27
⌅ [5b7e9947] AdvancedMH v0.5.1
[b5ca4192] AdvancedVI v0.1.6
[f5f396d3] ApproxBayes v0.3.2
[dce04be8] ArgCheck v2.3.0
⌅ [ec485272] ArnoldiMethod v0.1.0
⌅ [4fba245c] ArrayInterface v2.14.17
[30b0a656] ArrayInterfaceCore v0.1.22
[13072b0f] AxisAlgorithms v1.0.1
[39de3d68] AxisArrays v0.4.6
⌅ [6e4b80f9] BenchmarkTools v0.7.0
⌅ [76274a88] Bijectors v0.8.12
[b99e7846] BinaryProvider v0.5.10
⌃ [a134a8b2] BlackBoxOptim v0.5.0
[2d3116d5] Bridge v0.11.6
[46d747a0] BridgeSDEInference v0.3.2
[fa961155] CEnum v0.4.2
[a9c8d775] CPUTime v1.0.0
⌅ [00ebfdb7] CSTParser v2.5.0
[49dc2e85] Calculus v0.5.1
⌅ [082447d4] ChainRules v0.8.25
⌅ [d360d2e6] ChainRulesCore v0.10.13
[523fee87] CodecBzip2 v0.7.2
[944b1d66] CodecZlib v0.7.0
[35d6a980] ColorSchemes v3.19.0
[3da002f7] ColorTypes v0.11.4
[c3611d14] ColorVectorSpace v0.9.9
[5ae59095] Colors v0.12.8
[861a8166] Combinatorics v1.0.2
[a80b9123] CommonMark v0.8.6
[38540f10] CommonSolve v0.2.1
[bbf7d656] CommonSubexpressions v0.3.0
⌅ [34da2185] Compat v3.46.0
[b152e2b5] CompositeTypes v0.1.2
[8f4d0f93] Conda v1.7.0
[88cd18e8] ConsoleProgressMonitor v0.1.2
[187b0558] ConstructionBase v1.4.1
[d38c429a] Contour v0.6.2
[587fd27a] CovarianceEstimation v0.2.8
[a8cc5b0e] Crayons v4.1.1
[9a962f9c] DataAPI v1.12.0
[864edb3b] DataStructures v0.18.13
[e2d170a0] DataValueInterfaces v1.0.0
[39dd38d3] Dierckx v0.5.2
⌅ [2b5f629d] DiffEqBase v6.70.0
⌃ [ebbdde9d] DiffEqBayes v2.25.0
[459566f4] DiffEqCallbacks v2.24.2
⌅ [c894b116] DiffEqJump v6.15.1
[77a26b50] DiffEqNoiseProcess v5.13.1
⌃ [1130ab10] DiffEqParamEstim v1.22.0
⌃ [41bf760c] DiffEqSensitivity v6.50.0
[163ba53b] DiffResults v1.1.0
⌃ [b552c78f] DiffRules v1.5.0
⌅ [b4f34e82] Distances v0.9.2
⌅ [31c24e10] Distributions v0.23.12
⌃ [ced4e74d] DistributionsAD v0.6.29
⌅ [ffbed154] DocStringExtensions v0.8.6
⌅ [e30172f5] Documenter v0.26.3
[5b8099bc] DomainSets v0.5.13
[bbc10e6e] DynamicHMC v3.3.0
⌅ [366bfd00] DynamicPPL v0.9.0
⌅ [cad2338a] EllipticalSliceSampling v0.2.2
[7da242da] Enzyme v0.10.12
[f151be2c] EnzymeCore v0.1.0
[d4d017d3] ExponentialUtilities v1.19.0
[e2ba6199] ExprTools v0.1.8
[c87230d0] FFMPEG v0.4.1
[7a1cc6ca] FFTW v1.5.0
⌅ [7034ab61] FastBroadcast v0.1.8
[9aa1b823] FastClosures v0.3.2
⌅ [1a297f60] FillArrays v0.9.7
⌃ [6a86dc24] FiniteDiff v2.13.1
[53c48c17] FixedPointNumbers v0.8.4
[59287772] Formatting v0.4.2
[f6369f11] ForwardDiff v0.10.32
[069b7b12] FunctionWrappers v1.1.3
[77dc65aa] FunctionWrappersWrappers v0.1.1
⌃ [0c68f7d7] GPUArrays v8.3.2
[46192b85] GPUArraysCore v0.1.2
[61eb1bfa] GPUCompiler v0.16.4
[28b8d3ca] GR v0.69.5
⌅ [43dcc890] GaussianDistributions v0.3.3
[c145ed77] GenericSchur v0.5.3
⌅ [af5da776] GlobalSensitivity v1.3.3
[42e2da0e] Grisu v1.0.2
⌅ [cd3eb016] HTTP v0.9.17
[7073ff75] IJulia v1.23.3
⌅ [b5f81e59] IOCapture v0.1.1
[7869d1d1] IRTools v0.4.7
[615f187c] IfElse v0.1.1
[d25df0c9] Inflate v0.1.3
[83e8ac13] IniFile v0.5.1
[842dd82b] InlineStrings v1.2.2
[505f98c9] InplaceOps v0.3.0
[18e54dd8] IntegerMathUtils v0.1.0
⌅ [a98d9a8b] Interpolations v0.12.10
[8197267c] IntervalSets v0.7.3
[d8418881] Intervals v1.8.0
[41ab1584] InvertedIndices v1.1.0
[92d709cd] IrrationalConstants v0.1.1
[c8e1da08] IterTools v1.4.0
[42fd0dbc] IterativeSolvers v0.9.2
[82899510] IteratorInterfaceExtensions v1.0.0
[1019f520] JLFzf v0.1.5
[692b3bcd] JLLWrappers v1.4.1
[682c06a0] JSON v0.21.3
⌅ [7d188eb4] JSONSchema v0.3.4
⌃ [4076af6c] JuMP v0.21.5
⌅ [98e50ef6] JuliaFormatter v0.13.10
[5ab0869b] KernelDensity v0.6.5
[929cbde3] LLVM v4.14.0
[b964fa9f] LaTeXStrings v1.3.0
⌃ [2ee39098] LabelledArrays v1.6.6
[23fbe1c1] Latexify v0.15.17
[a5e1c1ea] LatinHypercubeSampling v1.8.0
[73f95e8e] LatticeRules v0.0.1
⌅ [1fad7336] LazyStack v0.0.8
⌅ [7f8f8fb0] LearnBase v0.4.1
⌃ [1d6d02ad] LeftChildRightSiblingTrees v0.1.3
⌅ [6f1fad26] Libtask v0.4.2
[093fc24a] LightGraphs v1.3.5
⌃ [d3d80556] LineSearches v7.1.1
⌅ [6fdf6af0] LogDensityProblems v0.10.6
⌃ [2ab3a3ac] LogExpFunctions v0.3.0
[e6f89c97] LoggingExtras v0.4.9
⌅ [2fda8390] LsqFit v0.12.1
⌅ [c7f686f2] MCMCChains v4.14.1
[e80e1ace] MLJModelInterface v1.7.0
[1914dd2f] MacroTools v0.5.10
⌅ [dbb5928d] MappedArrays v0.3.0
⌅ [b8f27783] MathOptInterface v0.9.22
[fdba3010] MathProgBase v0.7.8
[739be429] MbedTLS v1.1.6
[442fdcdd] Measures v0.3.1
[e1d29d7a] Missings v1.0.2
[78c3b35d] Mocking v0.7.3
⌅ [961ee093] ModelingToolkit v5.20.0
[46d2c3a1] MuladdMacro v0.2.2
⌅ [d8a4904e] MutableArithmetics v0.2.22
[d41bc354] NLSolversBase v7.8.2
⌃ [76087f3c] NLopt v0.6.3
[2774e3e8] NLsolve v4.5.1
⌅ [872c559c] NNlib v0.7.34
⌅ [77ba4419] NaNMath v0.3.7
[86f7a689] NamedArrays v0.9.6
⌃ [356022a1] NamedDims v0.2.37
[c020b1a1] NaturalSort v1.0.0
[8913a72c] NonlinearSolve v0.3.22
[d8793406] ObjectFile v0.3.7
[6fe1bfb0] OffsetArrays v1.12.8
[429524aa] Optim v1.7.3
[87e2bd06] OptimBase v2.0.2
[bac558e1] OrderedCollections v1.4.1
⌅ [1dea7af3] OrdinaryDiffEq v5.55.1
⌅ [90014a1f] PDMats v0.10.1
[d96e819e] Parameters v0.12.3
[69de0a69] Parsers v2.4.2
⌅ [06bb1623] PenaltyFunctions v0.2.1
[b98c9c47] Pipe v1.3.0
[f3e62ec7] PkgCleanup v0.1.0 https://github.com/giordano/PkgCleanup.jl#main
[ccf2f8ad] PlotThemes v3.1.0
⌃ [995b91a9] PlotUtils v1.2.0
[91a5bcdd] Plots v1.35.3
[e409e4f3] PoissonRandom v0.4.1
⌅ [f27b6e38] Polynomials v2.0.17
[85a6dd25] PositiveFactorizations v0.2.4
⌅ [d236fae5] PreallocationTools v0.2.3
[21216c6a] Preferences v1.3.0
⌅ [08abe8d2] PrettyTables v1.3.1
[27ebfcd6] Primes v0.5.3
[33c8b6b6] ProgressLogging v0.1.4
[92933f4c] ProgressMeter v1.7.2
[1fd47b50] QuadGK v2.5.0
[8a4e6c94] QuasiMonteCarlo v0.2.13
[74087812] Random123 v1.6.0
[fb686558] RandomExtensions v0.4.3
[e6cf234a] RandomNumbers v1.5.3
[b3c3ace0] RangeArrays v0.3.2
[c84ed2f1] Ratios v0.4.3
[3cdcf5f2] RecipesBase v1.3.0
[01d81517] RecipesPipeline v0.6.7
⌃ [731186ca] RecursiveArrayTools v2.17.2
⌅ [f2c3362d] RecursiveFactorization v0.1.0
⌅ [189a3867] Reexport v0.2.0
[05181044] RelocatableFolders v1.0.0
[ae029012] Requires v1.3.0
[ae5879a3] ResettableStacks v1.1.1
⌃ [37e2e3b7] ReverseDiff v1.9.0
[79098fc4] Rmath v0.7.0
[b0e4dd01] RollingFunctions v0.6.2
[7e49a35a] RuntimeGeneratedFunctions v0.5.3
[1bc83da4] SafeTestsets v0.0.1
[0bca4576] SciMLBase v1.62.0
[30f210dd] ScientificTypesBase v3.0.0
[6c6a2e73] Scratch v1.1.1
⌅ [efcf1570] Setfield v0.7.1
[992d4aef] Showoff v1.0.3
[699a6c99] SimpleTraits v0.9.4
[66db9d55] SnoopPrecompile v1.0.1
[ed01d8cd] Sobol v1.5.0
[b85f4697] SoftGlobalScope v1.1.0
[a2af1166] SortingAlgorithms v1.0.1
⌃ [47a9eef4] SparseDiffTools v1.13.2
[d4ead438] SpatialIndexing v0.1.3
⌅ [276daf66] SpecialFunctions v0.10.3
[860ef19b] StableRNGs v1.0.0
⌅ [90137ffa] StaticArrays v0.12.5
[1e83bf80] StaticArraysCore v1.4.0
[64bff920] StatisticalTraits v3.2.0
[82ae8749] StatsAPI v1.5.0
[2913bbd2] StatsBase v0.33.21
⌅ [4c63d2b9] StatsFuns v0.9.7
⌃ [789caeaf] StochasticDiffEq v6.40.0
[5e0ebb24] Strided v1.2.3
⌅ [09ab397b] StructArrays v0.5.1
[53d494c1] StructIO v0.3.0
⌅ [d1185830] SymbolicUtils v0.11.0
⌅ [0c5d862f] Symbolics v0.1.32
[3783bdb8] TableTraits v1.0.1
[bd369af6] Tables v1.10.0
⌃ [02d47bb6] TensorCast v0.4.3
[62fd8b95] TensorCore v0.1.1
[5d786b92] TerminalLoggers v0.1.6
[f269a46b] TimeZones v1.9.0
[a759f4b9] TimerOutputs v0.5.21
⌅ [0796e94c] Tokenize v0.5.13
⌃ [9f7883ad] Tracker v0.2.20
[2c80a279] Trajectories v0.2.2
[3bb67fe8] TranscodingStreams v0.9.9
⌅ [84d833dd] TransformVariables v0.4.1
⌃ [24ddb15e] TransmuteDims v0.1.12
[592b5752] Trapz v2.0.3
[a2a6695c] TreeViews v0.3.0
[9d95972d] TupleTools v1.3.0
⌅ [fce5fe82] Turing v0.14.1
[5c2747f8] URIs v1.4.0
[3a884ed6] UnPack v1.0.2
[1cfade01] UnicodeFun v0.4.1
[1986cc42] Unitful v1.12.0
[41fe7b60] Unzip v0.2.0
[81def892] VersionParsing v1.3.0
⌅ [19fa3120] VertexSafeGraphs v0.1.2
[efce3f68] WoodburyMatrices v0.5.5
[c2297ded] ZMQ v1.2.1
⌃ [e88e6eb3] Zygote v0.6.17
[700de1a5] ZygoteRules v0.2.2
[6e34b625] Bzip2_jll v1.0.8+0
[83423d85] Cairo_jll v1.16.1+1
[cd4c43a9] Dierckx_jll v0.1.0+0
[7cc45869] Enzyme_jll v0.0.43+0
[2e619515] Expat_jll v2.4.8+0
[b22a6f82] FFMPEG_jll v4.4.2+2
[f5851436] FFTW_jll v3.3.10+0
[a3f928ae] Fontconfig_jll v2.13.93+0
[d7e528f0] FreeType2_jll v2.10.4+0
[559328eb] FriBidi_jll v1.0.10+0
[0656b61e] GLFW_jll v3.3.8+0
[d2c73de3] GR_jll v0.69.1+0
[78b55507] Gettext_jll v0.21.0+0
[7746bdde] Glib_jll v2.74.0+1
[3b182d85] Graphite2_jll v1.3.14+0
[2e76f6c2] HarfBuzz_jll v2.8.1+1
[1d5cc7b8] IntelOpenMP_jll v2018.0.3+2
[aacddb02] JpegTurbo_jll v2.1.2+0
[c1c5ebd0] LAME_jll v3.100.1+0
[88015f11] LERC_jll v3.0.0+1
[dad2f222] LLVMExtra_jll v0.0.16+0
[dd4b983a] LZO_jll v2.10.1+0
[e9f186c6] Libffi_jll v3.2.2+1
[d4300ac3] Libgcrypt_jll v1.8.7+0
[7e76a0d4] Libglvnd_jll v1.3.0+3
[7add5ba3] Libgpg_error_jll v1.42.0+0
[94ce4f54] Libiconv_jll v1.16.1+1
[4b2f31a3] Libmount_jll v2.35.0+0
[89763e89] Libtiff_jll v4.4.0+0
[38a345b3] Libuuid_jll v2.36.0+0
[856f044c] MKL_jll v2022.1.0+0
[079eb43e] NLopt_jll v2.7.1+0
[e7412a2a] Ogg_jll v1.3.5+1
[458c3c95] OpenSSL_jll v1.1.18+0
[efe28fd5] OpenSpecFun_jll v0.5.5+0
[91d4177d] Opus_jll v1.3.2+0
[30392449] Pixman_jll v0.40.1+0
[ea2cea3b] Qt5Base_jll v5.15.3+1
[f50d1b31] Rmath_jll v0.3.0+0
[a2964d1f] Wayland_jll v1.19.0+0
[2381bf8a] Wayland_protocols_jll v1.25.0+0
[02c8fc9c] XML2_jll v2.9.14+0
[aed1982a] XSLT_jll v1.1.34+0
[4f6342f7] Xorg_libX11_jll v1.6.9+4
[0c0b7dd1] Xorg_libXau_jll v1.0.9+4
[935fb764] Xorg_libXcursor_jll v1.2.0+4
[a3789734] Xorg_libXdmcp_jll v1.1.3+4
[1082639a] Xorg_libXext_jll v1.3.4+4
[d091e8ba] Xorg_libXfixes_jll v5.0.3+4
[a51aa0fd] Xorg_libXi_jll v1.7.10+4
[d1454406] Xorg_libXinerama_jll v1.1.4+4
[ec84b674] Xorg_libXrandr_jll v1.5.2+4
[ea2f1a96] Xorg_libXrender_jll v0.9.10+4
[14d82f49] Xorg_libpthread_stubs_jll v0.1.0+3
[c7cfdc94] Xorg_libxcb_jll v1.13.0+3
[cc61e674] Xorg_libxkbfile_jll v1.1.0+4
[12413925] Xorg_xcb_util_image_jll v0.4.0+1
[2def613f] Xorg_xcb_util_jll v0.4.0+1
[975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
[0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
[c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
[35661453] Xorg_xkbcomp_jll v1.4.2+4
[33bec58e] Xorg_xkeyboard_config_jll v2.27.0+4
[c5fb5394] Xorg_xtrans_jll v1.4.0+3
[8f1865be] ZeroMQ_jll v4.3.4+0
[3161d3a3] Zstd_jll v1.5.2+0
⌅ [214eeab7] fzf_jll v0.29.0+0
[a4ae2306] libaom_jll v3.4.0+0
[0ac62f75] libass_jll v0.15.1+0
[f638f0a6] libfdk_aac_jll v2.0.2+0
[b53b4c65] libpng_jll v1.6.38+0
[a9144af2] libsodium_jll v1.0.20+0
[f27f6e37] libvorbis_jll v1.3.7+1
[1270edf5] x264_jll v2021.5.5+0
[dfaa095f] x265_jll v3.5.0+0
[d8fb68d0] xkbcommon_jll v1.4.1+0
[0dad84c5] ArgTools v1.1.1
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[f43a241f] Downloads v1.6.0
[7b1f6079] FileWatching
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[4af54fe1] LazyArtifacts
[b27032c2] LibCURL v0.6.3
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[ca575930] NetworkOptions v1.2.0
[44cfe95a] Pkg v1.8.0
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA v0.7.0
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays
[10745b16] Statistics
[4607b0f0] SuiteSparse
[fa267f1f] TOML v1.0.0
[a4e569a6] Tar v1.10.1
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[e66e0078] CompilerSupportLibraries_jll v0.5.2+0
[deac9b47] LibCURL_jll v7.84.0+0
[29816b5a] LibSSH2_jll v1.10.2+0
[c8ffd9c3] MbedTLS_jll v2.28.0+0
[14a3606d] MozillaCACerts_jll v2022.2.1
[4536629a] OpenBLAS_jll v0.3.20+0
[efcefdf7] PCRE2_jll v10.40.0+0
[83775a58] Zlib_jll v1.2.12+3
[8e850b90] libblastrampoline_jll v5.1.1+0
[8e850ede] nghttp2_jll v1.48.0+0
[3f19e933] p7zip_jll v17.4.0+0
Info Packages marked with ⌃ and ⌅ have new versions available, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use status --outdated -m

(@v1.8) pkg>

following is my code:

using Bridge
using StaticArrays
using BridgeSDEInference
using BridgeSDEInference: EulerMaruyamaBounded
using Random, LinearAlgebra, Distributions
using DiffEqParamEstim
using DiffEqBayes
using RecursiveArrayTools
using Plots
using Optim
using NLopt
using OrdinaryDiffEq, DiffEqParamEstim, JuMP, NLopt, Plots
using Distributions
using BlackBoxOptim
const State = SArray{Tuple{2},T,1,2} where {T};

FOLLOWING IS MY ERROR

ERROR: LoadError: UndefVarError: SciMLProblem not defined
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base .\Base.jl:31
[2] top-level scope
@ C:\Users\viren.julia\packages\DiffEqParamEstim\CEtDL\src\build_loss_objective.jl:27
[3] include(mod::Module, _path::String)
@ Base .\Base.jl:419
[4] include(x::String)
@ DiffEqParamEstim C:\Users\viren.julia\packages\DiffEqParamEstim\CEtDL\src\DiffEqParamEstim.jl:1
[5] top-level scope
@ C:\Users\viren.julia\packages\DiffEqParamEstim\CEtDL\src\DiffEqParamEstim.jl:26
[6] include
@ .\Base.jl:419 [inlined]
[7] 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
[8] top-level scope
@ stdin:1
in expression starting at C:\Users\viren.julia\packages\DiffEqParamEstim\CEtDL\src\build_loss_objective.jl:27
in expression starting at C:\Users\viren.julia\packages\DiffEqParamEstim\CEtDL\src\DiffEqParamEstim.jl:1
in expression starting at stdin:1
Failed to precompile DiffEqParamEstim [1130ab10-4a5a-5621-a13d-e4788d82bd4c] to C:\Users\viren.julia\compiled\v1.8\DiffEqParamEstim\jl_F743.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)
@ 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
[9] eval
@ .\boot.jl:368 [inlined]
[10] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
@ Base .\loading.jl:1428

Virendra_Sheoran · October 14, 2022, 1:48pm

following is my status --outdated -m

(@v1.8) pkg> status --outdated -m
Status C:\Users\viren\.julia\environments\v1.8\Manifest.toml
⌅ [c3fe647b] AbstractAlgebra v0.15.1 (<v0.27.5): SymbolicUtils, Symbolics
⌃ [621f4979] AbstractFFTs v1.0.1 (<v1.2.1)
⌅ [80f14c24] AbstractMCMC v1.0.1 (<v4.1.3): AdvancedMH, DynamicPPL, EllipticalSliceSampling, MCMCChains, Turing
⌅ [1520ce14] AbstractTrees v0.3.4 (<v0.4.2): LeftChildRightSiblingTrees, ModelingToolkit, SymbolicUtils
⌅ [0bf59076] AdvancedHMC v0.2.27 (<v0.3.6): Turing
⌅ [5b7e9947] AdvancedMH v0.5.1 (<v0.6.8): Turing
⌅ [ec485272] ArnoldiMethod v0.1.0 (<v0.2.0): LightGraphs
⌅ [4fba245c] ArrayInterface v2.14.17 (<v6.0.23): DiffEqBase, DiffEqJump, EllipticalSliceSampling, LabelledArrays, ModelingToolkit, OrdinaryDiffEq, PreallocationTools, RecursiveArrayTools, SparseDiffTools, StochasticDiffEq
⌅ [6e4b80f9] BenchmarkTools v0.7.0 (<v1.3.1): LogDensityProblems
⌅ [76274a88] Bijectors v0.8.12 (<v0.10.6): DynamicPPL, Turing
⌃ [a134a8b2] BlackBoxOptim v0.5.0 (<v0.6.1)
⌅ [00ebfdb7] CSTParser v2.5.0 (<v3.3.6): JuliaFormatter
⌅ [082447d4] ChainRules v0.8.25 (<v1.44.7): DistributionsAD, Zygote
⌅ [d360d2e6] ChainRulesCore v0.10.13 (<v1.15.6): ChainRules, DiffEqSensitivity, DistributionsAD, Zygote
⌅ [34da2185] Compat v3.46.0 (<v4.3.0): Bijectors, BlackBoxOptim, ChainRules, ChainRulesCore, DiffEqJump, DistributionsAD, MCMCChains, Mocking, NNlib, SparseDiffTools
⌅ [2b5f629d] DiffEqBase v6.70.0 (<v6.105.1): DiffEqSensitivity, OrdinaryDiffEq
⌃ [ebbdde9d] DiffEqBayes v2.25.0 (<v3.1.0)
⌅ [c894b116] DiffEqJump v6.15.1 (<v8.6.3): ModelingToolkit, StochasticDiffEq
⌃ [1130ab10] DiffEqParamEstim v1.22.0 (<v1.26.0)
⌃ [41bf760c] DiffEqSensitivity v6.50.0 (<v6.79.0)
⌃ [b552c78f] DiffRules v1.5.0 (<v1.11.1)
⌅ [b4f34e82] Distances v0.9.2 (<v0.10.7): ApproxBayes
⌅ [31c24e10] Distributions v0.23.12 (<v0.25.76): AdvancedMH, ApproxBayes, Bijectors, BlackBoxOptim, Bridge, BridgeSDEInference, DiffEqParamEstim, DynamicPPL, EllipticalSliceSampling, GaussianDistributions, Turing
⌃ [ced4e74d] DistributionsAD v0.6.29 (<v0.6.43)
⌅ [ffbed154] DocStringExtensions v0.8.6 (<v0.9.1): AdvancedHMC, DiffEqBase, DiffEqBayes, Documenter, LogDensityProblems, LogExpFunctions, ModelingToolkit, OrdinaryDiffEq, RecursiveArrayTools, StochasticDiffEq, Symbolics, TransformVariables, Turing
⌅ [e30172f5] Documenter v0.26.3 (<v0.27.23): JuliaFormatter
⌅ [366bfd00] DynamicPPL v0.9.0 (<v0.20.2): Turing
⌅ [cad2338a] EllipticalSliceSampling v0.2.2 (<v1.0.0): Turing
⌅ [7034ab61] FastBroadcast v0.1.8 (<v0.2.1): DiffEqBase
⌅ [1a297f60] FillArrays v0.9.7 (<v0.13.4): Distributions, DistributionsAD, StochasticDiffEq, Zygote
⌃ [6a86dc24] FiniteDiff v2.13.1 (<v2.15.0)
⌃ [0c68f7d7] GPUArrays v8.3.2 (<v8.5.0)
⌅ [43dcc890] GaussianDistributions v0.3.3 (<v0.5.2): BridgeSDEInference
⌅ [af5da776] GlobalSensitivity v1.3.3 (<v2.1.1): DiffEqSensitivity
⌅ [cd3eb016] HTTP v0.9.17 (<v1.4.1): JSONSchema
⌅ [b5f81e59] IOCapture v0.1.1 (<v0.2.2): Documenter
⌅ [a98d9a8b] Interpolations v0.12.10 (<v0.14.6): BridgeSDEInference
⌅ [7d188eb4] JSONSchema v0.3.4 (<v1.0.1): MathOptInterface
⌃ [4076af6c] JuMP v0.21.5 (<v1.3.1)
⌅ [98e50ef6] JuliaFormatter v0.13.10 (<v1.0.12): ModelingToolkit
⌃ [2ee39098] LabelledArrays v1.6.6 (<v1.12.0)
⌅ [1fad7336] LazyStack v0.0.8 (<v0.1.1): TensorCast
⌅ [7f8f8fb0] LearnBase v0.4.1 (<v0.6.1): PenaltyFunctions
⌃ [1d6d02ad] LeftChildRightSiblingTrees v0.1.3 (<v0.2.0)
⌅ [6f1fad26] Libtask v0.4.2 (<v0.8.2): Turing
⌃ [d3d80556] LineSearches v7.1.1 (<v7.2.0)
⌅ [6fdf6af0] LogDensityProblems v0.10.6 (<v1.0.2): DiffEqBayes, Turing
⌃ [2ab3a3ac] LogExpFunctions v0.3.0 (<v0.3.18)
⌅ [2fda8390] LsqFit v0.12.1 (<v0.13.0): DiffEqParamEstim
⌅ [c7f686f2] MCMCChains v4.14.1 (<v5.5.0): Turing
⌅ [dbb5928d] MappedArrays v0.3.0 (<v0.4.1): Bijectors
⌅ [b8f27783] MathOptInterface v0.9.22 (<v1.8.2): JuMP, NLopt
⌅ [961ee093] ModelingToolkit v5.20.0 (<v8.27.0): DiffEqBayes
⌅ [d8a4904e] MutableArithmetics v0.2.22 (<v1.0.5): JuMP, MathOptInterface, Polynomials
⌃ [76087f3c] NLopt v0.6.3 (<v0.6.5)
⌅ [872c559c] NNlib v0.7.34 (<v0.8.9): Bijectors
⌅ [77ba4419] NaNMath v0.3.7 (<v1.0.1): DiffRules, DistributionsAD, JuMP, LineSearches, ModelingToolkit, ReverseDiff, SymbolicUtils, Symbolics, Zygote
⌃ [356022a1] NamedDims v0.2.37 (<v1.1.0)
⌅ [1dea7af3] OrdinaryDiffEq v5.55.1 (<v6.29.0): StochasticDiffEq
⌅ [90014a1f] PDMats v0.10.1 (<v0.11.16): Distributions
⌅ [06bb1623] PenaltyFunctions v0.2.1 (<v0.3.0): DiffEqParamEstim
⌃ [995b91a9] PlotUtils v1.2.0 (<v1.3.1)
⌅ [f27b6e38] Polynomials v2.0.17 (<v3.2.0): Bridge
⌅ [d236fae5] PreallocationTools v0.2.3 (<v0.4.4): DiffEqParamEstim
⌅ [08abe8d2] PrettyTables v1.3.1 (<v2.1.2): MCMCChains
⌃ [731186ca] RecursiveArrayTools v2.17.2 (<v2.32.0)
⌅ [f2c3362d] RecursiveFactorization v0.1.0 (<v0.2.12): DiffEqBase
⌅ [189a3867] Reexport v0.2.0 (<v1.2.2): Turing
⌃ [37e2e3b7] ReverseDiff v1.9.0 (<v1.14.3)
⌅ [efcf1570] Setfield v0.7.1 (<v1.1.1): DiffEqBase, ModelingToolkit, SymbolicUtils, Symbolics
⌃ [47a9eef4] SparseDiffTools v1.13.2 (<v1.27.0)
⌅ [276daf66] SpecialFunctions v0.10.3 (<v2.1.7): Bridge, Distributions, DistributionsAD, MCMCChains, ModelingToolkit, ReverseDiff, StatsFuns, SymbolicUtils, Symbolics, Turing, Zygote
⌅ [90137ffa] StaticArrays v0.12.5 (<v1.5.9): BridgeSDEInference, Distributions, Interpolations
⌅ [4c63d2b9] StatsFuns v0.9.7 (<v1.0.1): AdvancedHMC, Bijectors, Distributions, DistributionsAD, MCMCChains, Turing
⌃ [789caeaf] StochasticDiffEq v6.40.0 (<v6.54.0)
⌅ [09ab397b] StructArrays v0.5.1 (<v0.6.12): DiffEqBayes
⌅ [d1185830] SymbolicUtils v0.11.0 (<v0.19.11): ModelingToolkit, Symbolics
⌅ [0c5d862f] Symbolics v0.1.32 (<v4.11.1): ModelingToolkit
⌃ [02d47bb6] TensorCast v0.4.3 (<v0.4.6)
⌅ [0796e94c] Tokenize v0.5.13 (<v0.5.24): JuliaFormatter
⌃ [9f7883ad] Tracker v0.2.20 (<v0.2.22)
⌅ [84d833dd] TransformVariables v0.4.1 (<v0.7.0): DiffEqBayes, LogDensityProblems
⌃ [24ddb15e] TransmuteDims v0.1.12 (<v0.1.14)
⌅ [fce5fe82] Turing v0.14.1 (<v0.21.12): DiffEqBayes
⌅ [19fa3120] VertexSafeGraphs v0.1.2 (<v0.2.0): SparseDiffTools
⌃ [e88e6eb3] Zygote v0.6.17 (<v0.6.49)
⌅ [214eeab7] fzf_jll v0.29.0+0 (<v0.30.0+0): JLFzf

(@v1.8) pkg>

nilshg · October 14, 2022, 1:51pm

I don’t think there’s more we can do - we’ve now said multiple times that you should operate in a fresh environment, and report back if there are any errors then. You clearly have loads of packages in your default environment, with most of them on some massively outdated versions.

If you don’t know how environments work, read the Pkg.jl docs, specifically the section here:

https://pkgdocs.julialang.org/v1/environments/

ChrisRackauckas · October 14, 2022, 5:49pm

No, not delete Julia. Have you deleted the folder C:\Users\viren\.julia\? There’s still a ton of packages in your system that have no explanation for it. The example has 3 packages: using Turing, DifferentialEquations, StatsPlots (LinearAlgebra is a standard library). Those are all that should show up when you do ]st.

Virendra_Sheoran · October 15, 2022, 6:10am

After deleting the folder C:\Users\viren\.julia\ i have followed instructions given on the following link
https://pkgdocs.julialang.org/v1/environments/

Following is the code i have run till now

julia> mkdir(“Juliawork”)
“Juliawork”

julia> cd(“Juliawork”)

(@v1.8) pkg> activate
Activating project at C:\Users\viren\.julia\environments\v1.8

(@v1.8) pkg> st
Installing known registries into C:\Users\viren\.julia
Status C:\Users\viren\.julia\environments\v1.8\Project.toml (empty project)

(@v1.8) pkg> st
Status C:\Users\viren\.julia\environments\v1.8\Project.toml (empty project)

(@v1.8) pkg>

Now i am following every instructions given by you…

following are the packages which i need to use :
using Bridge
using StaticArrays
using BridgeSDEInference
using BridgeSDEInference: EulerMaruyamaBounded
using Random, LinearAlgebra, Distributions
using DiffEqParamEstim
using DiffEqBayes
using RecursiveArrayTools
using Plots
using Optim
using NLopt
using OrdinaryDiffEq, DiffEqParamEstim, JuMP, NLopt, Plots
using Distributions
using BlackBoxOptim

Kindly tell me what should be my next step… I am quite new to this lnguage and facing tremendous issue in the beginning itself…Please guys help me

digital_carver · October 15, 2022, 7:31pm

There’s a dot after the activate in the manual page, and is missing here (it’s easy to miss, to be fair). activate takes an argument that specifies what to activate, and the . means to activate the current directory as a project. Without the ., it activates just the default Julia environment, which you were already in.

You can see that the (@v1.8) at the beginning didn’t change after you ran the command. That’s the name of the current environment, and once you run the correct command activate ., that should change to (Juliaworks) instead.

Once you’ve activated the correct environment, you can install the packages you need, and try running the code. The original issue shouldn’t happen anymore since you have a modern Julia version compatible with the latest Bridge, but BridgeSDEInference seems like it hasn’t been updated in a while, and is likely to cause version conflicts again. None of the code you’ve shown previously seem to use either Bridge or BridgeSDEInference, so you can skip them if you don’t need them for this project.

If you do need all these packages together for some other part of a tutorial, best to create a new thread asking for that tutorial to be updated with more current packages.

If you want to be really careful, you can also check and make sure after each package installation whether the latest version (or something pretty close) has gotten installed. But the rest of the packages here seem like they should be able to work together fine.

ChrisRackauckas · October 15, 2022, 8:20pm

I cannot think of a single use that actually needs this combination of packages. Are you very very sure you “need” to use that combination? That seems to be testing all algorithms for estimation rather than actually doing inference

If you need that combination, then you’d need to update the compats on the Bridge ones.