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InitError: expected Downloads [...] to exist in manifest when precompiling for tests #51727

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@fatteneder

Description

Noticed when testing Dynesty.jl on #49866, but problem also appears on master.
Problem does not appear on v1.9, v1.10-beta.
Problem only occurs on runnig test Dynesty for the first time, every other test Dynesty call then proceeds normally.

The error does not seem to be logged (or appear?) on the daily PkgEval: https://s3.amazonaws.com/julialang-reports/nanosoldier/pkgeval/by_date/2023-10/14/Dynesty.primary.log

Stacktrace `test Dynesty`
(@v1.11) pkg> test Dynesty
     Testing Dynesty
      Status `/tmp/jl_0jVR0Y/Project.toml`
  [31c24e10] Distributions v0.25.102
  [eb527566] Dynesty v0.3.1
  [8dfed614] Test
      Status `/tmp/jl_0jVR0Y/Manifest.toml`
  [49dc2e85] Calculus v0.5.1
  [34da2185] Compat v4.10.0
  [992eb4ea] CondaPkg v0.2.21
  [9a962f9c] DataAPI v1.15.0
  [864edb3b] DataStructures v0.18.15
  [e2d170a0] DataValueInterfaces v1.0.0
  [31c24e10] Distributions v0.25.102
  [ffbed154] DocStringExtensions v0.9.3
  [fa6b7ba4] DualNumbers v0.6.8
  [eb527566] Dynesty v0.3.1
  [1a297f60] FillArrays v1.6.1
  [34004b35] HypergeometricFunctions v0.3.23
  [92d709cd] IrrationalConstants v0.2.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.5.0
  [0f8b85d8] JSON3 v1.13.2
  [2ab3a3ac] LogExpFunctions v0.3.26
  [1914dd2f] MacroTools v0.5.11
  [0b3b1443] MicroMamba v0.1.14
  [e1d29d7a] Missings v1.1.0
  [77ba4419] NaNMath v1.0.2
  [bac558e1] OrderedCollections v1.6.2
  [90014a1f] PDMats v0.11.26
  [69de0a69] Parsers v2.7.2
  [fa939f87] Pidfile v1.3.0
  [aea7be01] PrecompileTools v1.2.0
  [21216c6a] Preferences v1.4.1
  [6099a3de] PythonCall v0.9.14
  [1fd47b50] QuadGK v2.9.1
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [79098fc4] Rmath v0.7.1
  [6c6a2e73] Scratch v1.2.0
  [a2af1166] SortingAlgorithms v1.1.1
  [276daf66] SpecialFunctions v2.3.1
  [10745b16] Statistics v1.11.0
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.2
  [4c63d2b9] StatsFuns v1.3.0
  [856f2bd8] StructTypes v1.10.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.11.0
  [e17b2a0c] UnsafePointers v1.0.0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [f50d1b31] Rmath_jll v0.4.0+0
  [f8abcde7] micromamba_jll v1.4.9+0
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [6462fe0b] Sockets
  [2f01184e] SparseArrays v1.11.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.0.5+1
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.7.1+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.24+0
  [05823500] OpenLibm_jll v0.8.1+2
  [bea87d4a] SuiteSparse_jll v7.2.0+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.8.0+1
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2
  Activating project at `/tmp/jl_0jVR0Y`
Precompiling project...
  ✓ PythonCall
  ✗ Dynesty
  1 dependency successfully precompiled in 15 seconds. 81 already precompiled.

ERROR: The following 1 direct dependency failed to precompile:

Dynesty [eb527566-0f3e-4aab-bb5f-9d2e403dba70]

Failed to precompile Dynesty [eb527566-0f3e-4aab-bb5f-9d2e403dba70] to "/home/flo/wd/julia/usr/share/julia/compiled/v1.11/Dynesty/jl_4XxIkh".
ERROR: LoadError: InitError: expected package `Downloads [f43a241f]` to exist in the manifest (use `resolve` to populate the manifest)
Stacktrace:
  [1] pkgerror(::String, ::Vararg{String})
    @ Pkg.Types ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/Types.jl:70
  [2] package_info
    @ Pkg.API ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:58 [inlined]
  [3] #9
    @ Pkg.API ./none:0 [inlined]
  [4] iterate
    @ Base ./generator.jl:47 [inlined]
  [5] _all(f::Base.var"#392#394", itr::Base.Generator{Vector{Pkg.Types.PackageSpec}, Pkg.API.var"#9#10"{Pkg.Types.EnvCache}}, ::Colon)
    @ Base ./reduce.jl:1296
  [6] all
    @ Base ./reduce.jl:1288 [inlined]
  [7] Dict(kv::Base.Generator{Vector{Pkg.Types.PackageSpec}, Pkg.API.var"#9#10"{Pkg.Types.EnvCache}})
    @ Base ./dict.jl:119
  [8] dependencies
    @ Pkg.API ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:88 [inlined]
  [9] dependencies()
    @ Pkg.API ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:85
 [10] _resolve_find_dependencies(io::Any, load_path::Any)
    @ CondaPkg ~/wd/julia/usr/share/julia/packages/CondaPkg/22jbl/src/resolve.jl:109
 [11] resolve(; force::Bool, io::IO, interactive::Bool, dry_run::Bool)
    @ CondaPkg ~/wd/julia/usr/share/julia/packages/CondaPkg/22jbl/src/resolve.jl:466
 [12] resolve()
    @ CondaPkg ~/wd/julia/usr/share/julia/packages/CondaPkg/22jbl/src/resolve.jl:405
 [13] envdir()
    @ CondaPkg ~/wd/julia/usr/share/julia/packages/CondaPkg/22jbl/src/env.jl:70
 [14] init_context()
    @ PythonCall.C ~/wd/julia/usr/share/julia/packages/PythonCall/qTEA1/src/cpython/context.jl:63
 [15] __init__()
    @ PythonCall.C ~/wd/julia/usr/share/julia/packages/PythonCall/qTEA1/src/cpython/CPython.jl:21
 [16] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1135
 [17] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1123
 [18] _include_from_serialized(pkg::Base.PkgId,      TestingPrecompilation of test environment failed. Continuing to tests9
0     Testingm pRunning tests...a
th::String, ocachepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1068
 [19] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
    @ Base ./loading.jl:1582
 [20] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1995
 [21] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1872
 [22] #invoke_in_world#3
    @ Base ./essentials.jl:933 [inlined]
 [23] invoke_in_world
    @ Base ./essentials.jl:930 [inlined]
 [24] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1863
 [25] macro expansion
    @ Base ./loading.jl:1801 [inlined]
 [26] macro expansion
    @ Base ./lock.jl:267 [inlined]
 [27] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1762
 [28] #invoke_in_world#3
    @ Base ./essentials.jl:933 [inlined]
 [29] invoke_in_world
    @ Base ./essentials.jl:930 [inlined]
 [30] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1755
 [31] include
    @ Base ./Base.jl:497 [inlined]
 [32] 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:2318
 [33] top-level scope
    @ stdin:3
during initialization of module C
in expression starting at /home/flo/wd/julia/usr/share/julia/packages/Dynesty/mYEKN/src/Dynesty.jl:1
in expression starting at stdin:3

caused by: expected package `Downloads [f43a241f]` to exist in the manifest (use `resolve` to populate the manifest)
Stacktrace:
  [1] pkgerror(::String, ::Vararg{String})
    @ Pkg.Types ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/Types.jl:70
  [2] package_info
    @ Pkg.API ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:58 [inlined]
  [3] #9
    @ Pkg.API ./none:0 [inlined]
  [4] iterate
    @ Base ./generator.jl:47 [inlined]
  [5] Dict{Base.UUID, Pkg.API.PackageInfo}(kv::Base.Generator{Vector{Pkg.Types.PackageSpec}, Pkg.API.var"#9#10"{Pkg.Types.EnvCache}})
    @ Base ./dict.jl:91
  [6] dict_with_eltype
    @ Base ./abstractdict.jl:582 [inlined]
  [7] dict_with_eltype
    @ Base ./abstractdict.jl:589 [inlined]
  [8] Dict(kv::Base.Generator{Vector{Pkg.Types.PackageSpec}, Pkg.API.var"#9#10"{Pkg.Types.EnvCache}})
    @ Base ./dict.jl:117
  [9] dependencies
    @ Pkg.API ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:88 [inlined]
 [10] dependencies()
    @ Pkg.API ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:85
 [11] _resolve_find_dependencies(io::Any, load_path::Any)
    @ CondaPkg ~/wd/julia/usr/share/julia/packages/CondaPkg/22jbl/src/resolve.jl:109
 [12] resolve(; force::Bool, io::IO, interactive::Bool, dry_run::Bool)
    @ CondaPkg ~/wd/julia/usr/share/julia/packages/CondaPkg/22jbl/src/resolve.jl:466
 [13] resolve()
    @ CondaPkg ~/wd/julia/usr/share/julia/packages/CondaPkg/22jbl/src/resolve.jl:405
 [14] envdir()
    @ CondaPkg ~/wd/julia/usr/share/julia/packages/CondaPkg/22jbl/src/env.jl:70
 [15] init_context()
    @ PythonCall.C ~/wd/julia/usr/share/julia/packages/PythonCall/qTEA1/src/cpython/context.jl:63
 [16] __init__()
    @ PythonCall.C ~/wd/julia/usr/share/julia/packages/PythonCall/qTEA1/src/cpython/CPython.jl:21
 [17] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1135
 [18] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1123
 [19] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1068
 [20] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
    @ Base ./loading.jl:1582
 [21] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1995
 [22] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1872
 [23] #invoke_in_world#3
    @ Base ./essentials.jl:933 [inlined]
 [24] invoke_in_world
    @ Base ./essentials.jl:930 [inlined]
 [25] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1863
 [26] macro expansion
    @ Base ./loading.jl:1801 [inlined]
 [27] macro expansion
    @ Base ./lock.jl:267 [inlined]
 [28] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1762
 [29] #invoke_in_world#3
    @ Base ./essentials.jl:933 [inlined]
 [30] invoke_in_world
    @ Base ./essentials.jl:930 [inlined]
 [31] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1755
 [32] include
    @ Base ./Base.jl:497 [inlined]
 [33] 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:2318
 [34] top-level scope
    @ stdin:3




































tacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/Types.jl:70
 [2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, timing::Bool, _from_loading::Bool, kwargs::@Kwargs{io::Pkg.UnstableIO})
   @ Pkg.API ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:1643
 [3] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::Pkg.UnstableIO, kwargs::@Kwargs{warn_loaded::Bool})
   @ Pkg.API ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
 [4] precompile(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::Nothing, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::@Kwargs{warn_loaded::Bool})
   @ Pkg.API ~/wd/julia/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:174
 [5] top-level scope
   @ none:7
    CondaPkg Found dependencies: /home/flo/wd/julia/usr/share/julia/packages/PythonCall/qTEA1/CondaPkg.toml
    CondaPkg Found dependencies: /home/flo/wd/julia/usr/share/julia/packages/Dynesty/mYEKN/CondaPkg.toml
    CondaPkg Resolving changes
             + dynesty
             + libstdcxx-ng
             + python
    CondaPkg Creating environment
             │ /home/flo/wd/julia/usr/share/julia/artifacts/87052ac9aec71548f804b30280151288cb1ed40e/bin/micromamba
             │ -r /home/flo/wd/julia/usr/share/julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root
             │ create
             │ -y
             │ -p /tmp/jl_0jVR0Y/.CondaPkg/env
             │ --override-channels
             │ --no-channel-priority
             │ dynesty[version='>=2.1']
             │ libstdcxx-ng[version='>=3.4,<13.0',channel='conda-forge']
             │ python[version='>=3.6,<=3.10']
             │ python[version='>=3.7,<4',channel='conda-forge',build='*cpython*']
             └ -c conda-forge
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache

Transaction

  Prefix: /tmp/jl_0jVR0Y/.CondaPkg/env

  Updating specs:

   - dynesty[version='>=2.1']
   - conda-forge::libstdcxx-ng[version='>=3.4,<13.0']
   - python[version='>=3.6,<=3.10']
   - conda-forge::python[version='>=3.7,<4',build=*cpython*]


  Package               Version  Build                Channel           Size
──────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────

  + libstdcxx-ng         12.3.0  h0f45ef3_2           conda-forge     Cached
  + _libgcc_mutex           0.1  conda_forge          conda-forge     Cached
  + python_abi             3.10  4_cp310              conda-forge     Cached
  + ld_impl_linux-64       2.40  h41732ed_0           conda-forge     Cached
  + ca-certificates   2023.7.22  hbcca054_0           conda-forge     Cached
  + libgomp              13.2.0  h807b86a_2           conda-forge     Cached
  + _openmp_mutex           4.5  2_gnu                conda-forge     Cached
  + libgcc-ng            13.2.0  h807b86a_2           conda-forge     Cached
  + xorg-libxdmcp         1.1.3  h7f98852_0           conda-forge     Cached
  + pthread-stubs           0.4  h36c2ea0_1001        conda-forge     Cached
  + libdeflate             1.19  hd590300_0           conda-forge     Cached
  + lerc                  4.0.0  h27087fc_0           conda-forge     Cached
  + libjpeg-turbo         3.0.0  hd590300_1           conda-forge     Cached
  + xz                    5.2.6  h166bdaf_0           conda-forge     Cached
  + openssl               3.1.3  hd590300_0           conda-forge     Cached
  + ncurses                 6.4  hcb278e6_0           conda-forge     Cached
  + libuuid              2.38.1  h0b41bf4_0           conda-forge     Cached
  + libnsl                2.0.1  hd590300_0           conda-forge     Cached
  + libffi                3.4.2  h7f98852_5           conda-forge     Cached
  + bzip2                 1.0.8  h7f98852_4           conda-forge     Cached
  + libbrotlicommon       1.1.0  hd590300_1           conda-forge     Cached
  + xorg-libxau          1.0.11  hd590300_0           conda-forge     Cached
  + libwebp-base          1.3.2  hd590300_0           conda-forge     Cached
  + libgfortran5         13.2.0  ha4646dd_2           conda-forge     Cached
  + libzlib              1.2.13  hd590300_5           conda-forge     Cached
  + readline                8.2  h8228510_1           conda-forge     Cached
  + libbrotlienc          1.1.0  hd590300_1           conda-forge     Cached
  + libbrotlidec          1.1.0  hd590300_1           conda-forge     Cached
  + libxcb                 1.15  h0b41bf4_0           conda-forge     Cached
  + libgfortran-ng       13.2.0  h69a702a_2           conda-forge     Cached
  + zstd                  1.5.5  hfc55251_0           conda-forge     Cached
  + libsqlite            3.43.2  h2797004_0           conda-forge     Cached
  + libpng               1.6.39  h753d276_0           conda-forge     Cached
  + tk                   8.6.13  h2797004_0           conda-forge     Cached
  + brotli-bin            1.1.0  hd590300_1           conda-forge     Cached
  + libopenblas          0.3.24  pthreads_h413a1c8_0  conda-forge     Cached
  + libtiff               4.6.0  ha9c0a0a_2           conda-forge     Cached
  + sqlite               3.43.2  h2c6b66d_0           conda-forge     Cached
  + freetype             2.12.1  h267a509_2           conda-forge     Cached
  + brotli                1.1.0  hd590300_1           conda-forge     Cached
  + libblas               3.9.0  19_linux64_openblas  conda-forge     Cached
  + lcms2                  2.15  hb7c19ff_3           conda-forge     Cached
  + openjpeg              2.5.0  h488ebb8_3           conda-forge     Cached
  + libcblas              3.9.0  19_linux64_openblas  conda-forge     Cached
  + liblapack             3.9.0  19_linux64_openblas  conda-forge     Cached
  + tzdata                2023c  h71feb2d_0           conda-forge     Cached
  + python               3.10.0  h543edf9_3_cpython   conda-forge     Cached
  + wheel                0.41.2  pyhd8ed1ab_0         conda-forge     Cached
  + setuptools           68.2.2  pyhd8ed1ab_0         conda-forge     Cached
  + pip                    23.3  pyhd8ed1ab_0         conda-forge     Cached
  + six                  1.16.0  pyh6c4a22f_0         conda-forge     Cached
  + munkres               1.1.4  pyh9f0ad1d_0         conda-forge     Cached
  + pyparsing             3.1.1  pyhd8ed1ab_0         conda-forge     Cached
  + packaging              23.2  pyhd8ed1ab_0         conda-forge     Cached
  + cycler               0.12.1  pyhd8ed1ab_0         conda-forge     Cached
  + certifi           2023.7.22  pyhd8ed1ab_0         conda-forge     Cached
  + python-dateutil       2.8.2  pyhd8ed1ab_0         conda-forge     Cached
  + numpy                1.26.0  py310hb13e2d6_0      conda-forge     Cached
  + unicodedata2         15.1.0  py310h2372a71_0      conda-forge     Cached
  + pillow               10.1.0  py310h01dd4db_0      conda-forge     Cached
  + kiwisolver            1.4.5  py310hd41b1e2_1      conda-forge     Cached
  + contourpy             1.1.1  py310hd41b1e2_1      conda-forge     Cached
  + scipy                1.11.3  py310hb13e2d6_1      conda-forge     Cached
  + fonttools            4.43.1  py310h2372a71_0      conda-forge     Cached
  + matplotlib-base       3.8.0  py310h62c0568_2      conda-forge     Cached
  + dynesty               2.1.2  pyhd8ed1ab_0         conda-forge     Cached

  Summary:

  Install: 66 packages

  Total download: 0 B

──────────────────────────────────────────────────────────────────────────────



Transaction starting
Linking libstdcxx-ng-12.3.0-h0f45ef3_2
Linking _libgcc_mutex-0.1-conda_forge
Linking python_abi-3.10-4_cp310
Linking ld_impl_linux-64-2.40-h41732ed_0
Linking ca-certificates-2023.7.22-hbcca054_0
Linking libgomp-13.2.0-h807b86a_2
Linking _openmp_mutex-4.5-2_gnu
Linking libgcc-ng-13.2.0-h807b86a_2
Linking xorg-libxdmcp-1.1.3-h7f98852_0
Linking pthread-stubs-0.4-h36c2ea0_1001
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Transaction finished

To activate this environment, use:

    micromamba activate /tmp/jl_0jVR0Y/.CondaPkg/env

Or to execute a single command in this environment, use:

    micromamba run -p /tmp/jl_0jVR0Y/.CondaPkg/env mycommand

┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead.
│   caller = ip:0x0
└ @ Core :-1

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    regressionRegression in behavior compared to a previous versionstdlibJulia's standard library

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