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Compile cache permission denied #57254

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maleadt opened this issue Dec 17, 2024 · 3 comments
Open

Compile cache permission denied #57254

maleadt opened this issue Dec 17, 2024 · 3 comments

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@maleadt
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maleadt commented Dec 17, 2024

On Metal.jl, we encountered the following permission error during precompilation:

ERROR: SystemError: opening file "/Users/julia/.julia/compiled/v1.11/Metal/ACDsk_tBsmV.ji": Permission denied

Full log:

     Testing Metal
      Status `/private/var/tmp/agent-tempdirs/default-macmini-aarch64-5.0/tmp/jl_ezdPsi/Project.toml`
  [79e6a3ab] Adapt v4.1.1
  [ab4f0b2a] BFloat16s v0.5.0
  [6e4b80f9] BenchmarkTools v1.5.0
  [0c68f7d7] GPUArrays v11.1.0
  [63c18a36] KernelAbstractions v0.9.31
  [929cbde3] LLVM v9.1.3
  [dde4c033] Metal v1.4.0 `/Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/build/default-macmini-aarch64-5-0/julialang/metal-dot-jl`
  [e86c9b32] ObjectiveC v3.1.0
  [276daf66] SpecialFunctions v2.5.0
  [90137ffa] StaticArrays v1.9.8
  [10745b16] Statistics v1.11.1
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [de0858da] Printf v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [8dfed614] Test v1.11.0
      Status `/private/var/tmp/agent-tempdirs/default-macmini-aarch64-5.0/tmp/jl_ezdPsi/Manifest.toml`
  [79e6a3ab] Adapt v4.1.1
  [a9b6321e] Atomix v1.0.1
  [ab4f0b2a] BFloat16s v0.5.0
  [6e4b80f9] BenchmarkTools v1.5.0
  [fa961155] CEnum v0.5.0
  [523fee87] CodecBzip2 v0.8.4
  [ffbed154] DocStringExtensions v0.9.3
  [e2ba6199] ExprTools v0.1.10
  [0c68f7d7] GPUArrays v11.1.0
  [46192b85] GPUArraysCore v0.2.0
  [61eb1bfa] GPUCompiler v1.0.1
  [92d709cd] IrrationalConstants v0.2.2
  [692b3bcd] JLLWrappers v1.6.1
  [682c06a0] JSON v0.21.4
  [63c18a36] KernelAbstractions v0.9.31
  [929cbde3] LLVM v9.1.3
  [2ab3a3ac] LogExpFunctions v0.3.29
  [1914dd2f] MacroTools v0.5.13
  [dde4c033] Metal v1.4.0 `/Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/build/default-macmini-aarch64-5-0/julialang/metal-dot-jl`
  [d8793406] ObjectFile v0.4.2
  [e86c9b32] ObjectiveC v3.1.0
  [69de0a69] Parsers v2.8.1
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [6c6a2e73] Scratch v1.2.1
  [276daf66] SpecialFunctions v2.5.0
  [90137ffa] StaticArrays v1.9.8
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [53d494c1] StructIO v0.3.1
  [a759f4b9] TimerOutputs v0.5.26
  [3bb67fe8] TranscodingStreams v0.11.3
  [013be700] UnsafeAtomics v0.3.0
  [6e34b625] Bzip2_jll v1.0.8+2
  [2e619515] Expat_jll v2.6.4+1
  [f52de702] LLVMDowngrader_jll v0.5.0+0
  [dad2f222] LLVMExtra_jll v0.0.34+0
  [7106de7a] LibMPDec_jll v2.5.1+0
⌅ [e9f186c6] Libffi_jll v3.2.2+2
  [458c3c95] OpenSSL_jll v3.0.15+1
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [93d3a430] Python_jll v3.10.14+0
  [76ed43ae] SQLite_jll v3.47.2+0
  [ffd25f8a] XZ_jll v5.6.3+0
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf v1.11.0
  [9abbd945] Profile v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [f489334b] StyledStrings v1.11.0
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [05823500] OpenLibm_jll v0.8.1+2
  [bea87d4a] SuiteSparse_jll v7.7.0+0
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.59.0+0
  [3f19e933] p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
ERROR: SystemError: opening file "/Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/depots/5cd495a2-4a16-4674-ae02-c839447744bb/compiled/v1.11/Metal/ACDsk_tBsmV.ji": Permission denied
Stacktrace:
  [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
    @ Base ./error.jl:176
  [2] systemerror
    @ ./error.jl:175 [inlined]
  [3] open(fname::String; lock::Bool, read::Bool, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing)
    @ Base ./iostream.jl:295
  [4] open
    @ ./iostream.jl:277 [inlined]
  [5] open(fname::String, mode::String; lock::Bool)
    @ Base ./iostream.jl:358
  [6] open
    @ ./iostream.jl:357 [inlined]
  [7] (::Base.var"#sort_by#1080")(path::String)
    @ Base ./loading.jl:1166
  [8] _broadcast_getindex_evalf
    @ ./broadcast.jl:673 [inlined]
  [9] _broadcast_getindex
    @ ./broadcast.jl:646 [inlined]
 [10] getindex
    @ ./broadcast.jl:605 [inlined]
 [11] macro expansion
    @ ./broadcast.jl:968 [inlined]
 [12] macro expansion
    @ ./simdloop.jl:77 [inlined]
 [13] copyto!
    @ ./broadcast.jl:967 [inlined]
 [14] copyto!
    @ ./broadcast.jl:920 [inlined]
 [15] copy
    @ ./broadcast.jl:892 [inlined]
 [16] materialize
    @ ./broadcast.jl:867 [inlined]
 [17] find_all_in_cache_path(pkg::Base.PkgId, DEPOT_PATH::Vector{String})
    @ Base ./loading.jl:1191
 [18] find_all_in_cache_path
    @ ./loading.jl:1146 [inlined]
 [19] JuliaLang/Pkg.jl#28
    @ ./precompilation.jl:874 [inlined]
 [20] get!(default::Base.Precompilation.var"#28#68"{Base.PkgId}, h::Dict{Base.PkgId, Vector{String}}, key::Base.PkgId)
    @ Base ./dict.jl:458
 [21] _precompilepkgs(pkgs::Vector{String}, internal_call::Bool, strict::Bool, warn_loaded::Bool, timing::Bool, _from_loading::Bool, configs::Vector{Pair{Cmd, Base.CacheFlags}}, io::IOContext{IO}, fancyprint::Bool)
    @ Base.Precompilation ./precompilation.jl:874
 [22] #precompilepkgs#10
    @ ./precompilation.jl:409 [inlined]
 [23] (::Pkg.API.var"#225#226"{Bool, Bool, Bool, Bool, Bool, Pair{Cmd, Base.CacheFlags}, Vector{Pkg.Types.PackageSpec}})()
    @ Pkg.API /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/API.jl:1152
 [24] activate(f::Pkg.API.var"#225#226"{Bool, Bool, Bool, Bool, Bool, Pair{Cmd, Base.CacheFlags}, Vector{Pkg.Types.PackageSpec}}, new_project::String)
    @ Pkg.API /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/API.jl:1373
 [25] 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, configs::Pair{Cmd, Base.CacheFlags}, kwargs::@Kwargs{io::IOContext{IO}})
    @ Pkg.API /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/API.jl:1150
 [26] precompile
    @ /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/API.jl:1126 [inlined]
 [27] #precompile#118
    @ /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/API.jl:164 [inlined]
 [28] (::Pkg.Operations.var"#132#137"{Base.CacheFlags, Cmd, Pkg.Types.Context})()
    @ Pkg.Operations /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2061
 [29] activate(f::Pkg.Operations.var"#132#137"{Base.CacheFlags, Cmd, Pkg.Types.Context}, new_project::String)
    @ Pkg.API /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/API.jl:1373
 [30] (::Pkg.Operations.var"#131#136"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec})()
    @ Pkg.Operations /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2060
 [31] withenv(::Pkg.Operations.var"#131#136"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, ::Pair{String, String}, ::Vararg{Pair{String}})
    @ Base ./env.jl:265
 [32] (::Pkg.Operations.var"#118#123"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#131#136"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec})()
    @ Pkg.Operations /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1920
 [33] with_temp_env(fn::Pkg.Operations.var"#118#123"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#131#136"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec}, temp_env::String)
    @ Pkg.Operations /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1778
 [34] (::Pkg.Operations.var"#116#121"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#131#136"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, String})(tmp::String)
    @ Pkg.Operations /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1887
 [35] mktempdir(fn::Pkg.Operations.var"#116#121"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#131#136"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, String}, parent::String; prefix::String)
    @ Base.Filesystem ./file.jl:819
 [36] mktempdir(fn::Function, parent::String)
    @ Base.Filesystem ./file.jl:815
 [37] mktempdir
    @ ./file.jl:815 [inlined]
 [38] #sandbox#115
    @ /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1834 [inlined]
 [39] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
    @ Pkg.Operations /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2052
 [40] test
    @ /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1996 [inlined]
 [41] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}})
    @ Pkg.API /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/API.jl:475
 [42] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{coverage::Bool, julia_args::Cmd, test_args::Cmd})
    @ Pkg.API /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
 [43] test(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::Nothing, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::@Kwargs{coverage::Bool, julia_args::Cmd, test_args::Cmd})
    @ Pkg.API /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/julia_installs/bin/mac/aarch64/1.11/julia-1.11-latest-macaarch64/share/julia/stdlib/v1.11/Pkg/src/API.jl:174
 [44] top-level scope
    @ none:11
🚨 Error: The command exited with status 1

After logging in to the CI bot, the file exists and has bad permissions:

% ls -la /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/depots/5cd495a2-4a16-4674-ae02-c839447744bb/compiled/v1.11/Metal/ACDsk_tBsmV.ji
--w-------  1 julia  staff  21152 Dec 16 13:28 /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/depots/5cd495a2-4a16-4674-ae02-c839447744bb/compiled/v1.11/Metal/ACDsk_tBsmV.ji

I'm not sure how that would have happened. It's the only file with such permissions:

% find /Users/julia/.julia/scratchspaces/*/agent-cache/*/depots/*/compiled -perm 200
/Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-5.0/depots/5cd495a2-4a16-4674-ae02-c839447744bb/compiled/v1.11/Metal/ACDsk_tBsmV.ji

Should Pkg handle this more gracefully?
@maleadt maleadt mentioned this issue Dec 17, 2024
Merged
@maleadt
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maleadt commented Feb 4, 2025

Bump; this happened again, breaking Metal.jl CI.

https://buildkite.com/julialang/metal-dot-jl/builds/1665#0194cf1f-f0f2-49e3-af95-41261e20ab8e

julia@macmini-aarch64-3 ~ % ls -la /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-3.0/depots/5cd495a2-4a16-4674-ae02-c839447744bb/compiled/v1.11/Metal
total 119400
drwxr-xr-x  14 julia  staff       448 Feb  3 23:25 .
drwxr-xr-x  89 julia  staff      2848 Feb  3 14:12 ..
-rwxr-xr-x   1 julia  staff  14770928 Feb  3 07:01 ACDsk_Bcr7m.dylib
drwxr-xr-x   3 julia  staff        96 Feb  3 07:01 ACDsk_Bcr7m.dylib.dSYM
-rw-r--r--   1 julia  staff    573522 Feb  3 07:02 ACDsk_Bcr7m.ji
-rwxr-xr-x   1 julia  staff  14901344 Feb  3 07:03 ACDsk_RqvQU.dylib
drwxr-xr-x   3 julia  staff        96 Jan 28 21:35 ACDsk_RqvQU.dylib.dSYM
-rw-r--r--   1 julia  staff    573522 Feb  3 07:04 ACDsk_RqvQU.ji
-rwxr-xr-x   1 julia  staff  14917856 Feb  3 14:05 ACDsk_nveup.dylib
drwxr-xr-x   3 julia  staff        96 Jan 24 22:06 ACDsk_nveup.dylib.dSYM
--w-------   1 julia  staff     20578 Feb  3 14:05 ACDsk_nveup.ji
-rwxr-xr-x   1 julia  staff  14770928 Feb  3 14:03 ACDsk_xcPoO.dylib
drwxr-xr-x   3 julia  staff        96 Feb  3 14:03 ACDsk_xcPoO.dylib.dSYM
-rw-r--r--   1 julia  staff    575802 Feb  3 14:04 ACDsk_xcPoO.ji

Notice the one cache file with messed up permissions.

@KristofferC
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Does Pkg modify the precompile files at all? Base creates them so probably the problem is there?

@maleadt maleadt transferred this issue from JuliaLang/Pkg.jl Feb 4, 2025
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maleadt commented Feb 4, 2025

OK, transferred to Base.

@bvdmitri bvdmitri mentioned this issue Feb 26, 2025
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