`Pkg` workflow after Julia version update

I am on Ubuntu 22.04.03. I have installed Julia 1.10 using the curl command here. I want to update a project environment so that it uses Julia 1.10. However, upon activate . and instantiate, several packages fail to precompile. I suspect my workflow may be incorrect, but I could not find clear instructions (apologies if I missed something).

What is the recommended workflow to update projects to new versions of Julia?

You might need to update as well. If you can provide the error messages for the precompilation that would be useful. The failure to precompile message should have a note how to retrieve the stacktraces.

Thank you, @mkitti. If I install 1.10 and then activate . and update, I also get several errors at the precompilation stage. They all relate to AdaptStaticArraysExt.jl and AdaptStaticArraysCoreExt.jl. The warnings and errors I get start as follows (not copying the whole thing to save on space)

Warning: attempting to remove probably stale pidfile  339/361
│   path = "/home/joao/.julia/compiled/v1.10/Plots/ld3vC_RGXJy.ji.pidfile"
└ @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.10.0+0.x64.linux.gnu/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:244
┌ Warning: attempting to remove probably stale pidfile  355/361
│   path = "/home/joao/.julia/compiled/v1.10/Polyhedra/17i4E_RGXJy.ji.pidfile"
└ @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.10.0+0.x64.linux.gnu/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:244
  ✗ Adapt → AdaptStaticArraysExt
  ✗ ExactPredicates
  ✗ DelaunayTriangulation
  ✗ BlackBoxOptim → BlackBoxOptimRealtimePlotServerExt
  ✗ Makie
  ✗ LinearSolve
  ✗ LinearSolvePardiso
  ✗ NonlinearSolve
  346 dependencies successfully precompiled in 108 seconds. 117 already precompiled. 7 skipped during auto due to previous errors.
  14 dependencies had output during precompilation:

And then there are several errors related to AdaptStaticArraysExt.jl and AdaptStaticArraysCoreExt.jl. For instance:

MeshCat
│  ERROR: LoadError: ArgumentError: Package AdaptStaticArraysCoreExt does not have Adapt 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 AdaptStaticArraysCoreExt checked out for development and have
│    added Adapt 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 AdaptStaticArraysCoreExt
│  Stacktrace:
│   [1] macro expansion
│     @ Base ./loading.jl:1770 [inlined]
│   [2] macro expansion
│     @ Base ./lock.jl:267 [inlined]
│   [3] __require(into::Module, mod::Symbol)
│     @ Base ./loading.jl:1747
│   [4] #invoke_in_world#3
│     @ Base ./essentials.jl:921 [inlined]
│   [5] invoke_in_world
│     @ Base ./essentials.jl:918 [inlined]
│   [6] require(into::Module, mod::Symbol)
│     @ Base ./loading.jl:1740
│   [7] include
│     @ Base ./Base.jl:495 [inlined]
│   [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│     @ Base ./loading.jl:2216
│   [9] top-level scope
│     @ stdin:3
│  in expression starting at /home/joao/.julia/packages/Adapt/Ur60R/ext/AdaptStaticArraysExt.jl:1
│  in expression starting at stdin:3

If I follow the suggestion in the error message and ] instantiate nothing happens. Further update issues

Updating registry at `~/.julia/registries/General.toml`
  No Changes to `~/Dropbox/Research/dynamic_games/Project.toml`
  No Changes to `~/Dropbox/Research/dynamic_games/Manifest.toml`

However, when trying to using the packages required by my project, I get further errors related to AdaptStaticArraysExt and its sister package (omitting part of the error message for brevity):

Precompiling AdaptStaticArraysExt
        Info Given AdaptStaticArraysExt was explicitly requested, output will be shown live 
ERROR: LoadError: ArgumentError: Package AdaptStaticArraysCoreExt does not have Adapt 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 AdaptStaticArraysCoreExt checked out for development and have
  added Adapt 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 AdaptStaticArraysCoreExt
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1770 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
 [7] include
   @ Base ./Base.jl:495 [inlined]
 [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
   @ Base ./loading.jl:2216
 [9] top-level scope
   @ stdin:3
in expression starting at /home/joao/.julia/packages/Adapt/Ur60R/ext/AdaptStaticArraysExt.jl:1
in expression starting at stdin:3
  ✗ Adapt → AdaptStaticArraysExt
  0 dependencies successfully precompiled in 1 seconds. 6 already precompiled.
[ Info: Precompiling AdaptStaticArraysExt [e1699a77-9e31-5da8-bb3e-0a796f95f0a0]
ERROR: LoadError: ArgumentError: Package AdaptStaticArraysCoreExt does not have Adapt 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 AdaptStaticArraysCoreExt checked out for development and have
  added Adapt 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 AdaptStaticArraysCoreExt
Stacktrace:
 [1] macro expansion
   @ Base ./loading.jl:1770 [inlined]
 [2] macro expansion
   @ Base ./lock.jl:267 [inlined]
 [3] __require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1747
 [4] #invoke_in_world#3
   @ Base ./essentials.jl:921 [inlined]
 [5] invoke_in_world
   @ Base ./essentials.jl:918 [inlined]
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1740
 [7] include
   @ Base ./Base.jl:495 [inlined]
 [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
   @ Base ./loading.jl:2216
 [9] top-level scope
   @ stdin:3
in expression starting at /home/joao/.julia/packages/Adapt/Ur60R/ext/AdaptStaticArraysExt.jl:1
in expression starting at stdin:3

Sorry for the length of the reply! Any help would be much appreciated.

You have a lot of dependencies. Can you provide the output of

using Pkg
pkg"status"
pkg"status -m"

You likely have outdated packages.

The length is fine. Too little information is usually the problem.

1 Like

Is the takeaway that I should add Adapt?

FWIW the output of ] status is

⌃ [aae01518] BandedMatrices v0.17.18
  [6e4b80f9] BenchmarkTools v1.4.0
  [b99e7846] BinaryProvider v0.5.10
  [a134a8b2] BlackBoxOptim v0.6.3
  [336ed68f] CSV v0.10.12
  [324d7699] CategoricalArrays v0.10.8
  [a93c6f00] DataFrames v1.6.1
  [1313f7d8] DataFramesMeta v0.14.1
  [864edb3b] DataStructures v0.18.16
  [31a5f54b] Debugger v0.7.8
  [31c24e10] Distributions v0.25.107
  [2fe49d83] Expectations v1.9.2
⌃ [442a2c76] FastGaussQuadrature v0.4.5
  [26cc04aa] FiniteDifferences v0.12.31
  [f6369f11] ForwardDiff v0.10.36
  [38e38edf] GLM v1.9.0
  [60bf3e95] GLPK v1.1.3
  [87dc4568] HiGHS v1.7.5
⌅ [d1acc4aa] IntervalArithmetic v0.20.9
  [d2bf35a9] IntervalRootFinding v0.5.11
  [4076af6c] JuMP v1.18.1
  [2c470bb0] Kronecker v0.5.5
  [2b0e0bc5] LanguageServer v4.4.0
⌃ [d3d80556] LineSearches v7.1.1
⌅ [7ed4a6bd] LinearSolve v1.34.1
  [a6722589] LinearSolvePardiso v0.1.1
  [ee78f7c6] Makie v0.20.4
  [c03570c3] Memoize v0.4.4
⌃ [283c5d60] MeshCat v0.14.2
⌅ [76087f3c] NLopt v0.6.5
  [2774e3e8] NLsolve v4.5.1
⌃ [8913a72c] NonlinearSolve v1.0.1
  [429524aa] Optim v1.7.8
  [bac558e1] OrderedCollections v1.6.3
  [b51826c6] OrdinalMultinomialModels v0.4.5
  [e4faabce] PProf v3.1.0
  [d96e819e] Parameters v0.12.3
  [b98c9c47] Pipe v1.3.0
  [91a5bcdd] Plots v1.39.0
  [67491407] Polyhedra v0.7.6
  [d236fae5] PreallocationTools v0.4.17
  [c6596682] QuantileRegressions v0.1.11
  [6f49c342] RCall v0.13.18
  [295af30f] Revise v3.5.13
⌃ [f2b01f46] Roots v2.0.22
⌅ [727e6d20] SimpleNonlinearSolve v0.1.5
⌅ [276daf66] SpecialFunctions v1.8.8
⌅ [90137ffa] StaticArrays v0.12.6
  [814864de] StaticOptim v0.2.0
  [2913bbd2] StatsBase v0.34.2
  [4c63d2b9] StatsFuns v1.3.0
  [3eaba693] StatsModels v0.7.3
  [bd369af6] Tables v1.11.1
  [22787eb5] Term v2.0.5
  [ebf5ac4f] TexTables v0.2.7
  [a759f4b9] TimerOutputs v0.5.23
  [04da0e3b] TypeTree v0.3.0
  [ade2ca70] Dates
  [37e2e46d] LinearAlgebra
  [de0858da] Printf
  [9a3f8284] Random
  [9e88b42a] Serialization
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated`

and that of status -m is

[621f4979] AbstractFFTs v1.5.0
  [398f06c4] AbstractLattices v0.3.0
  [1520ce14] AbstractTrees v0.4.4
⌅ [79e6a3ab] Adapt v3.6.0
  [27a7e980] Animations v0.4.1
  [4fba245c] ArrayInterface v7.7.0
  [30b0a656] ArrayInterfaceCore v0.1.29
  [dd5226c6] ArrayInterfaceStaticArraysCore v0.1.4
⌃ [4c555306] ArrayLayouts v0.8.18
  [bf4720bc] AssetRegistry v0.1.0
  [67c07d97] Automa v1.0.2
  [13072b0f] AxisAlgorithms v1.1.0
  [39de3d68] AxisArrays v0.4.7
⌃ [aae01518] BandedMatrices v0.17.18
  [6e4b80f9] BenchmarkTools v1.4.0
  [9e28174c] BinDeps v1.0.2
  [b99e7846] BinaryProvider v0.5.10
  [62783981] BitTwiddlingConvenienceFunctions v0.1.5
  [a134a8b2] BlackBoxOptim v0.6.3
⌃ [ad839575] Blink v0.12.5
  [e1450e63] BufferedStreams v1.2.1
  [fa961155] CEnum v0.5.0
  [2a0fbf3d] CPUSummary v0.2.4
  [a9c8d775] CPUTime v1.0.0
  [96374032] CRlibm v1.0.1
  [00ebfdb7] CSTParser v3.4.0
  [336ed68f] CSV v0.10.12
  [49dc2e85] Calculus v0.5.1
  [7057c7e9] Cassette v0.3.12
  [324d7699] CategoricalArrays v0.10.8
  [8be319e6] Chain v0.5.0
  [d360d2e6] ChainRulesCore v1.19.0
  [fb6a15b2] CloseOpenIntervals v0.1.12
  [da1fd8a2] CodeTracking v1.3.5
  [523fee87] CodecBzip2 v0.8.1
  [944b1d66] CodecZlib v0.7.3
  [a2cac450] ColorBrewer v0.4.0
  [35d6a980] ColorSchemes v3.24.0
  [3da002f7] ColorTypes v0.11.4
  [c3611d14] ColorVectorSpace v0.10.0
  [5ae59095] Colors v0.12.10
  [861a8166] Combinatorics v1.0.2
  [a80b9123] CommonMark v0.8.12
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.0
  [34da2185] Compat v4.10.1
  [8f4d0f93] Conda v1.10.0
⌃ [187b0558] ConstructionBase v1.4.1
  [d38c429a] Contour v0.6.2
  [150eb455] CoordinateTransformations v0.6.3
  [587fd27a] CovarianceEstimation v0.2.11
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.15.0
  [a93c6f00] DataFrames v1.6.1
  [1313f7d8] DataFramesMeta v0.14.1
  [864edb3b] DataStructures v0.18.16
  [e2d170a0] DataValueInterfaces v1.0.0
  [31a5f54b] Debugger v0.7.8
  [927a84f5] DelaunayTriangulation v0.8.11
  [8bb1440f] DelimitedFiles v1.9.1
⌃ [2b5f629d] DiffEqBase v6.108.0
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [b4f34e82] Distances v0.10.11
  [31c24e10] Distributions v0.25.107
⌅ [ffbed154] DocStringExtensions v0.8.6
  [fa6b7ba4] DualNumbers v0.6.8
  [4e289a0a] EnumX v1.0.4
  [90fa49ef] ErrorfreeArithmetic v0.5.2
⌃ [429591f6] ExactPredicates v2.2.5
  [2fe49d83] Expectations v1.9.2
  [e2ba6199] ExprTools v0.1.10
  [411431e0] Extents v0.1.2
  [c87230d0] FFMPEG v0.4.1
  [7a1cc6ca] FFTW v1.7.2
  [7034ab61] FastBroadcast v0.2.8
⌃ [442a2c76] FastGaussQuadrature v0.4.5
⌅ [29a986be] FastLapackInterface v1.2.9
  [fa42c844] FastRounding v0.3.1
  [5789e2e9] FileIO v1.16.2
  [8fc22ac5] FilePaths v0.8.3
  [48062228] FilePathsBase v0.9.21
⌅ [1a297f60] FillArrays v0.13.11
⌃ [6a86dc24] FiniteDiff v2.17.0
  [26cc04aa] FiniteDifferences v0.12.31
  [53c48c17] FixedPointNumbers v0.8.4
  [08572546] FlameGraphs v1.0.0
  [59287772] Formatting v0.4.2
  [f6369f11] ForwardDiff v0.10.36
  [b38be410] FreeType v4.1.1
  [663a7486] FreeTypeAbstraction v0.10.1
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [de31a74c] FunctionalCollections v0.5.0
  [38e38edf] GLM v1.9.0
  [60bf3e95] GLPK v1.1.3
⌃ [46192b85] GPUArraysCore v0.1.5
⌅ [28b8d3ca] GR v0.72.10
  [14197337] GenericLinearAlgebra v0.3.11
  [cf35fbd7] GeoInterface v1.3.3
  [5c1252a2] GeometryBasics v0.4.9
  [c27321d9] Glob v1.3.1
  [3955a311] GridLayoutBase v0.10.0
  [42e2da0e] Grisu v1.0.2
⌅ [cd3eb016] HTTP v0.9.17
  [87dc4568] HiGHS v1.7.5
  [9fb69e20] Hiccup v0.2.2
  [eafb193a] Highlights v0.5.2
  [3e5b6fbb] HostCPUFeatures v0.1.16
  [34004b35] HypergeometricFunctions v0.3.23
  [615f187c] IfElse v0.1.1
  [2803e5a7] ImageAxes v0.6.11
  [c817782e] ImageBase v0.1.7
  [a09fc81d] ImageCore v0.10.1
  [82e4d734] ImageIO v0.6.7
  [bc367c6b] ImageMetadata v0.9.9
  [9b13fd28] IndirectArrays v1.0.0
  [d25df0c9] Inflate v0.1.4
  [83e8ac13] IniFile v0.5.1
  [842dd82b] InlineStrings v1.4.0
  [18e54dd8] IntegerMathUtils v0.1.2
  [a98d9a8b] Interpolations v0.15.1
⌅ [d1acc4aa] IntervalArithmetic v0.20.9
  [d2bf35a9] IntervalRootFinding v0.5.11
  [8197267c] IntervalSets v0.7.8
  [41ab1584] InvertedIndices v1.3.0
  [b6b21f68] Ipopt v1.6.0
⌅ [92d709cd] IrrationalConstants v0.1.1
  [f1662d9f] Isoband v0.1.1
  [c8e1da08] IterTools v1.10.0
  [42fd0dbc] IterativeSolvers v0.9.3
  [82899510] IteratorInterfaceExtensions v1.0.0
  [1019f520] JLFzf v0.1.7
  [692b3bcd] JLLWrappers v1.5.0
  [97c1335a] JSExpr v0.5.4
  [682c06a0] JSON v0.21.4
  [b9b8584e] JSONRPC v1.3.6
  [b835a17e] JpegTurbo v0.1.5
  [4076af6c] JuMP v1.18.1
  [98e50ef6] JuliaFormatter v1.0.45
  [aa1ae85d] JuliaInterpreter v0.9.28
  [ef3ab10e] KLU v0.4.1
  [5ab0869b] KernelDensity v0.6.8
  [2c470bb0] Kronecker v0.5.5
  [ba0b0d4f] Krylov v0.9.5
  [0b1a1467] KrylovKit v0.6.0
  [b964fa9f] LaTeXStrings v1.3.1
  [2b0e0bc5] LanguageServer v4.4.0
  [23fbe1c1] Latexify v0.16.1
  [10f19ff3] LayoutPointers v0.1.15
  [50d2b5c4] Lazy v0.15.1
  [8cdb02fc] LazyModules v0.3.1
  [1d6d02ad] LeftChildRightSiblingTrees v0.2.0
  [9c8b4983] LightXML v0.9.1
⌃ [d3d80556] LineSearches v7.1.1
  [9b3f67b0] LinearAlgebraX v0.2.5
⌅ [7ed4a6bd] LinearSolve v1.34.1
  [a6722589] LinearSolvePardiso v0.1.1
  [2ab3a3ac] LogExpFunctions v0.3.26
  [bdcacae8] LoopVectorization v0.12.166
  [6f1432cf] LoweredCodeUtils v2.4.3
  [1914dd2f] MacroTools v0.5.12
  [ee78f7c6] Makie v0.20.4
  [20f20a25] MakieCore v0.7.2
  [d125e4d3] ManualMemory v0.1.8
  [dbb5928d] MappedArrays v0.4.2
  [b8f27783] MathOptInterface v1.25.0
  [fdba3010] MathProgBase v0.7.8
  [0a4f8689] MathTeXEngine v0.5.7
  [739be429] MbedTLS v1.1.9
  [442fdcdd] Measures v0.3.2
  [c03570c3] Memoize v0.4.4
⌃ [283c5d60] MeshCat v0.14.2
  [e1d29d7a] Missings v1.1.0
  [78c3b35d] Mocking v0.7.7
  [7475f97c] Mods v2.2.2
  [e94cdb99] MosaicViews v0.3.4
  [99f44e22] MsgPack v1.2.1
  [46d2c3a1] MuladdMacro v0.2.4
  [3b2b4ff1] Multisets v0.4.4
  [ffc61752] Mustache v1.0.19
  [d8a4904e] MutableArithmetics v1.4.0
⌅ [a975b10e] Mux v0.7.6
  [1c23619d] MyterialColors v0.3.0
  [d41bc354] NLSolversBase v7.8.3
⌅ [76087f3c] NLopt v0.6.5
  [2774e3e8] NLsolve v4.5.1
⌅ [77ba4419] NaNMath v0.3.7
  [356022a1] NamedDims v1.2.1
  [f09324ee] Netpbm v1.1.1
⌃ [8913a72c] NonlinearSolve v1.0.1
  [510215fc] Observables v0.5.5
  [6fe1bfb0] OffsetArrays v1.13.0
  [52e1d378] OpenEXR v0.3.2
  [429524aa] Optim v1.7.8
  [bac558e1] OrderedCollections v1.6.3
  [b51826c6] OrdinalMultinomialModels v0.4.5
  [90014a1f] PDMats v0.11.31
  [f57f5aa1] PNGFiles v0.4.3
  [e4faabce] PProf v3.1.0
  [19eb6ba3] Packing v0.5.0
  [5432bcbf] PaddedViews v0.5.12
  [d96e819e] Parameters v0.12.3
⌃ [46dd5b70] Pardiso v0.5.0
  [69de0a69] Parsers v2.8.1
  [2ae35dd2] Permutations v0.4.19
  [fa939f87] Pidfile v1.3.0
  [b98c9c47] Pipe v1.3.0
  [eebad327] PkgVersion v0.3.3
  [ccf2f8ad] PlotThemes v3.1.0
  [995b91a9] PlotUtils v1.4.0
  [91a5bcdd] Plots v1.39.0
  [f517fe37] Polyester v0.7.9
  [1d0040c9] PolyesterWeave v0.2.1
  [647866c9] PolygonOps v0.1.2
  [67491407] Polyhedra v0.7.6
⌅ [f27b6e38] Polynomials v3.2.4
  [2dfb63ee] PooledArrays v1.4.3
  [85a6dd25] PositiveFactorizations v0.2.4
  [d236fae5] PreallocationTools v0.4.17
  [aea7be01] PrecompileTools v1.2.0
  [21216c6a] Preferences v1.4.1
  [08abe8d2] PrettyTables v2.3.1
  [27ebfcd6] Primes v0.5.5
  [33c8b6b6] ProgressLogging v0.1.4
  [92933f4c] ProgressMeter v1.9.0
  [3349acd9] ProtoBuf v1.0.15
  [4b34888f] QOI v1.0.0
  [1fd47b50] QuadGK v2.9.1
  [c6596682] QuantileRegressions v0.1.11
⌅ [94ee1d12] Quaternions v0.4.9
  [6f49c342] RCall v0.13.18
⌅ [df47a6cb] RData v0.8.3
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⌅ [e9f186c6] Libffi_jll v3.2.2+1
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Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`

Thanks!

I guess I had too many dependencies indeed. After dropping a few that were in fact not used by the project anymore, things seem to be working fine. Those dependencies were blocking the update of Adapt past v3.6.0, and thus preventing the resolution of the errors above. Lesson learned.

Thank you for the help, @mkitti. Much appreciated.

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