Circular dependencies January 2025

[johnomotani]

When I do a fresh install now (10/1/2025) with either Julia-1.10.7 or Julia-1.11.2, there is a problem due to 'circular dependencies'. Downgrading Accessors to v0.1.33 (from v0.1.40) and Roots to v2.2.0 (from v2.2.2) seems to fix this for now (I haven't checked whether this is the minimal change, it was just the first thing that seemed to work). Hopefully updates to those packages will resolve this soon.

[mrhardman]

On a recent fresh install, with these packages

(moment_kinetics) pkg> status
Status `~/excalibur-mk/moment_kinetics/Project.toml`
  [b964fa9f] LaTeXStrings v1.4.0
  [da04e1cc] MPI v0.20.22
  [3da0fdf6] MPIPreferences v0.1.11
  [442fdcdd] Measures v0.3.2
  [9b87118b] PackageCompiler v2.2.0
  [91a5bcdd] Plots v1.40.9
  [276daf66] SpecialFunctions v2.5.0
  [2913bbd2] StatsBase v0.34.4
  [b5ff72cc] moment_kinetics v0.1.0 `moment_kinetics`
  [8dfed614] Test

I have

(moment_kinetics) pkg> status -m
Status `~/excalibur-mk/moment_kinetics/Manifest.toml`
  [621f4979] AbstractFFTs v1.5.0
  [7d9f7c33] Accessors v0.1.39
  [79e6a3ab] Adapt v4.1.1
  [66dad0bd] AliasTables v1.1.3
  [c7e460c6] ArgParse v1.2.0
  [4fba245c] ArrayInterface v7.18.0
  [13072b0f] AxisAlgorithms v1.1.0
  [d1d4a3ce] BitFlags v0.1.9
  [d360d2e6] ChainRulesCore v1.25.0
  [da1fd8a2] CodeTracking v1.3.6
  [944b1d66] CodecZlib v0.7.6
  [35d6a980] ColorSchemes v3.27.1
  [3da002f7] ColorTypes v0.12.0
  [c3611d14] ColorVectorSpace v0.11.0
  [5ae59095] Colors v0.13.0
  [861a8166] Combinatorics v1.0.2
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.1
  [34da2185] Compat v4.16.0
  [a33af91c] CompositionsBase v0.1.2
  [f0e56b4a] ConcurrentUtilities v2.4.3
  [187b0558] ConstructionBase v1.5.8
  [d38c429a] Contour v0.6.3
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.18.20
  [8bb1440f] DelimitedFiles v1.9.1
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [31c24e10] Distributions v0.25.115
  [ffbed154] DocStringExtensions v0.9.3
  [460bff9d] ExceptionUnwrapping v0.1.11
  [e2ba6199] ExprTools v0.1.10
  [c87230d0] FFMPEG v0.4.2
  [7a1cc6ca] FFTW v1.8.0
  [442a2c76] FastGaussQuadrature v1.0.2
  [1a297f60] FillArrays v1.13.0
  [6a86dc24] FiniteDiff v2.26.2
  [53c48c17] FixedPointNumbers v0.8.5
  [1fa38f19] Format v1.3.7
  [f6369f11] ForwardDiff v0.10.38
  [28b8d3ca] GR v0.73.10
  [c27321d9] Glob v1.3.1
  [42e2da0e] Grisu v1.0.2
  [f67ccb44] HDF5 v0.17.2
  [cd3eb016] HTTP v1.10.15
  [34004b35] HypergeometricFunctions v0.3.25
  [18e54dd8] IntegerMathUtils v0.1.2
  [a98d9a8b] Interpolations v0.15.1
  [3587e190] InverseFunctions v0.1.17
  [92d709cd] IrrationalConstants v0.2.2
  [1019f520] JLFzf v0.1.9
  [692b3bcd] JLLWrappers v1.6.1
  [682c06a0] JSON v0.21.4
  [aa1ae85d] JuliaInterpreter v0.9.38
  [b964fa9f] LaTeXStrings v1.4.0
  [23fbe1c1] Latexify v0.16.5
  [3db4a2ba] LegendrePolynomials v0.4.5
  [2ab3a3ac] LogExpFunctions v0.3.29
  [e6f89c97] LoggingExtras v1.1.0
  [6f1432cf] LoweredCodeUtils v3.1.0
  [2fda8390] LsqFit v0.15.0
  [da04e1cc] MPI v0.20.22
  [3da0fdf6] MPIPreferences v0.1.11
  [1914dd2f] MacroTools v0.5.13
  [739be429] MbedTLS v1.1.9
  [442fdcdd] Measures v0.3.2
  [e1d29d7a] Missings v1.2.0
  [d41bc354] NLSolversBase v7.8.3
  [77ba4419] NaNMath v1.0.2
  [6fe1bfb0] OffsetArrays v1.15.0
  [4d8831e6] OpenSSL v1.4.3
  [bac558e1] OrderedCollections v1.7.0
  [90014a1f] PDMats v0.11.31
  [9b87118b] PackageCompiler v2.2.0
  [69de0a69] Parsers v2.8.1
  [b98c9c47] Pipe v1.3.0
  [eebad327] PkgVersion v0.3.3
  [ccf2f8ad] PlotThemes v3.3.0
  [995b91a9] PlotUtils v1.4.3
  [91a5bcdd] Plots v1.40.9
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [27ebfcd6] Primes v0.5.6
  [43287f4e] PtrArrays v1.2.1
  [1fd47b50] QuadGK v2.11.1
  [be4d8f0f] Quadmath v0.5.10
  [c84ed2f1] Ratios v0.4.5
  [3cdcf5f2] RecipesBase v1.3.4
  [01d81517] RecipesPipeline v0.6.12
  [189a3867] Reexport v1.2.2
  [05181044] RelocatableFolders v1.0.1
  [ae029012] Requires v1.3.0
  [295af30f] Revise v3.6.4
  [79098fc4] Rmath v0.8.0
  [f2b01f46] Roots v2.2.2
  [6c6a2e73] Scratch v1.2.1
  [efcf1570] Setfield v1.1.1
  [992d4aef] Showoff v1.0.3
  [777ac1f9] SimpleBufferStream v1.2.0
  [a2af1166] SortingAlgorithms v1.2.1
  [a0a7dd2c] SparseMatricesCSR v0.6.8
  [276daf66] SpecialFunctions v2.5.0
  [860ef19b] StableRNGs v1.0.2
  [90137ffa] StaticArrays v1.9.9
  [1e83bf80] StaticArraysCore v1.4.3
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.4
  [4c63d2b9] StatsFuns v1.3.2
  [62fd8b95] TensorCore v0.1.1
  [b718987f] TextWrap v1.0.2
  [a759f4b9] TimerOutputs v0.5.26
  [3bb67fe8] TranscodingStreams v0.11.3
  [5c2747f8] URIs v1.5.1
  [1cfade01] UnicodeFun v0.4.1
  [1986cc42] Unitful v1.21.1
  [45397f5d] UnitfulLatexify v1.6.4
  [41fe7b60] Unzip v0.2.0
  [efce3f68] WoodburyMatrices v1.0.0
  [b5ff72cc] moment_kinetics v0.1.0 `moment_kinetics`
  [6e34b625] Bzip2_jll v1.0.8+2
  [83423d85] Cairo_jll v1.18.2+1
  [ee1fde0b] Dbus_jll v1.14.10+0
  [2702e6a9] EpollShim_jll v0.0.20230411+1
  [2e619515] Expat_jll v2.6.4+1
⌅ [b22a6f82] FFMPEG_jll v4.4.4+1
  [f5851436] FFTW_jll v3.3.10+1
  [a3f928ae] Fontconfig_jll v2.15.0+0
  [d7e528f0] FreeType2_jll v2.13.3+1
  [559328eb] FriBidi_jll v1.0.16+0
  [0656b61e] GLFW_jll v3.4.0+2
  [d2c73de3] GR_jll v0.73.10+0
  [78b55507] Gettext_jll v0.21.0+0
  [7746bdde] Glib_jll v2.82.4+0
  [3b182d85] Graphite2_jll v1.3.14+1
⌃ [0234f1f7] HDF5_jll v1.14.2+1
  [2e76f6c2] HarfBuzz_jll v8.5.0+0
  [e33a78d0] Hwloc_jll v2.11.2+1
  [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
  [aacddb02] JpegTurbo_jll v3.1.0+0
  [c1c5ebd0] LAME_jll v3.100.2+0
  [88015f11] LERC_jll v4.0.0+1
  [1d63c593] LLVMOpenMP_jll v18.1.7+0
  [dd4b983a] LZO_jll v2.10.2+1
⌅ [e9f186c6] Libffi_jll v3.2.2+2
  [d4300ac3] Libgcrypt_jll v1.11.0+0
  [7e76a0d4] Libglvnd_jll v1.7.0+0
  [7add5ba3] Libgpg_error_jll v1.51.0+0
  [94ce4f54] Libiconv_jll v1.17.0+1
  [4b2f31a3] Libmount_jll v2.40.2+0
  [89763e89] Libtiff_jll v4.7.0+0
  [38a345b3] Libuuid_jll v2.40.2+0
  [856f044c] MKL_jll v2024.2.0+0
  [7cb0a576] MPICH_jll v4.2.3+0
  [f1f71cc9] MPItrampoline_jll v5.5.1+0
  [9237b28f] MicrosoftMPI_jll v10.1.4+3
  [e7412a2a] Ogg_jll v1.3.5+1
  [fe0851c0] OpenMPI_jll v5.0.6+0
  [458c3c95] OpenSSL_jll v3.0.15+1
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [91d4177d] Opus_jll v1.3.3+0
  [36c8627f] Pango_jll v1.55.5+0
⌅ [30392449] Pixman_jll v0.43.4+0
  [c0090381] Qt6Base_jll v6.7.1+1
  [629bc702] Qt6Declarative_jll v6.7.1+2
  [ce943373] Qt6ShaderTools_jll v6.7.1+1
  [e99dba38] Qt6Wayland_jll v6.7.1+1
  [f50d1b31] Rmath_jll v0.5.1+0
  [a44049a8] Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] Wayland_jll v1.21.0+2
  [2381bf8a] Wayland_protocols_jll v1.31.0+0
  [02c8fc9c] XML2_jll v2.13.5+0
  [aed1982a] XSLT_jll v1.1.42+0
  [ffd25f8a] XZ_jll v5.6.3+0
  [f67eecfb] Xorg_libICE_jll v1.1.1+0
  [c834827a] Xorg_libSM_jll v1.2.4+0
  [4f6342f7] Xorg_libX11_jll v1.8.6+1
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+1
  [935fb764] Xorg_libXcursor_jll v1.2.3+0
  [a3789734] Xorg_libXdmcp_jll v1.1.4+1
  [1082639a] Xorg_libXext_jll v1.3.6+1
  [d091e8ba] Xorg_libXfixes_jll v6.0.0+0
  [a51aa0fd] Xorg_libXi_jll v1.8.2+0
  [d1454406] Xorg_libXinerama_jll v1.1.5+0
  [ec84b674] Xorg_libXrandr_jll v1.5.4+0
  [ea2f1a96] Xorg_libXrender_jll v0.9.11+1
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.1+1
  [c7cfdc94] Xorg_libxcb_jll v1.17.0+1
  [cc61e674] Xorg_libxkbfile_jll v1.1.2+1
  [e920d4aa] Xorg_xcb_util_cursor_jll v0.1.4+0
  [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 v1.4.6+1
  [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] Xorg_xtrans_jll v1.5.0+1
  [3161d3a3] Zstd_jll v1.5.6+1
  [35ca27e7] eudev_jll v3.2.9+0
  [214eeab7] fzf_jll v0.56.3+0
  [1a1c6b14] gperf_jll v3.1.1+1
  [477f73a3] libaec_jll v1.1.2+0
  [a4ae2306] libaom_jll v3.9.0+0
  [0ac62f75] libass_jll v0.15.2+0
  [1183f4f0] libdecor_jll v0.2.2+0
  [2db6ffa8] libevdev_jll v1.11.0+0
  [f638f0a6] libfdk_aac_jll v2.0.3+0
  [36db933b] libinput_jll v1.18.0+0
  [b53b4c65] libpng_jll v1.6.44+0
  [f27f6e37] libvorbis_jll v1.3.7+2
  [009596ad] mtdev_jll v1.1.6+0
  [1317d2d5] oneTBB_jll v2021.12.0+0
⌅ [1270edf5] x264_jll v2021.5.5+0
⌅ [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+2
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.10.0
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+4
  [05823500] OpenLibm_jll v0.8.1+2
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2

I think you might be able to upgrade Roots to 2.2.2 and Accessors to 1.3.9.

[johnomotani]

Indeed Accessors v0.1.39 is fine. This seems to be a known bug JuliaObjects/Accessors.jl#192, although I think I saw a similar problem on Julia-1.11, which they say there should not be... seems to be fixed in Julia-1.11.2, and is supposed to be fixed in Julia-1.10.8.