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infinite loop Restart notebook (required) #2312

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SimonEnsemble opened this issue Oct 12, 2022 · 6 comments
Closed

infinite loop Restart notebook (required) #2312

SimonEnsemble opened this issue Oct 12, 2022 · 6 comments
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@fonsp
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package manager Pluto's built-in package manager

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@SimonEnsemble
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the problem in the Pluto notebook

I am experiencing an infinite loop of "Restart notebook (required)" requests (each time I click restart, it doesn't resolve).

this happens both (i) on a notebook I have launched before and (ii) upon creating a new notebook.

problem does not resolve after restarting Julia and/or Pluto.

the error message in the REPL from which Pluto is launched

┌ Warning: PlutoPkg: Failed to add/remove packages! Resetting package environment...
│   PLUTO_VERSION = v"0.19.13"
│   VERSION = v"1.8.2"
│   old_packages = String[]
│   new_packages =
│    4-element Vector{String}:
│     "Statistics"
│     "PlutoUI"
│     "CSV"
│     "DataFrames"
│   exception =
│    "/private/var/folders/mc/q4kv7qs121gc_0h42v317dyw0000gn/T/jl_uA6Zfj/Project.toml": No such file
│    Stacktrace:
│      [1] error(::String, ::String)
│        @ Base ./error.jl:44
│      [2] readstring
│        @ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/TOML/src/TOML.jl:21 [inlined]
│      [3] parsefile(f::String)
│        @ TOML /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/TOML/src/TOML.jl:43
│      [4] _modify_compat(f!::Pluto.PkgCompat.var"#27#28"{Pkg.Types.Context}, ctx::Pkg.Types.Context)
│        @ Pluto.PkgCompat ~/.julia/packages/Pluto/U4wvO/src/packages/PkgCompat.jl:408
│      [5] write_auto_compat_entries
│        @ ~/.julia/packages/Pluto/U4wvO/src/packages/PkgCompat.jl:430 [inlined]
│      [6] (::Pluto.var"#187#199"{Vector{String}, Pluto.Notebook, Pluto.IOListener})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:178
│      [7] withinteractive(f::Pluto.var"#187#199"{Vector{String}, Pluto.Notebook, Pluto.IOListener}, value::Bool)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:528
│      [8] #186
│        @ ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:150 [inlined]
│      [9] withio(f::Pluto.var"#186#198"{Vector{String}, Pluto.Notebook, Pluto.IOListener}, ctx::Pkg.Types.Context, io::IOContext{IOBuffer})
│        @ Pluto.PkgCompat ~/.julia/packages/Pluto/U4wvO/src/packages/PkgCompat.jl:129
│     [10] (::Pluto.var"#182#193"{Pluto.Notebook, Pluto.IOListener, Vector{String}, Vector{String}, Bool, Bool})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:149
│     [11] withtoken(f::Pluto.var"#182#193"{Pluto.Notebook, Pluto.IOListener, Vector{String}, Vector{String}, Bool, Bool}, token::Pluto.Token)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/evaluation/Tokens.jl:19
│     [12] sync_nbpkg_core(notebook::Pluto.Notebook, old_topology::Pluto.NotebookTopology, new_topology::Pluto.NotebookTopology; on_terminal_output::Pluto.var"#iocallback#209"{Pluto.ServerSession, Pluto.Notebook}, lag::Float64)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:112
│     [13] (::Pluto.var"#206#208"{Pluto.ServerSession, Pluto.Notebook, Pluto.NotebookTopology, Pluto.NotebookTopology})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:262
│     [14] #205
│        @ ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:253 [inlined]
│     [15] sync_nbpkg(session::Pluto.ServerSession, notebook::Pluto.Notebook, old_topology::Pluto.NotebookTopology, new_topology::Pluto.NotebookTopology; save::Bool, take_token::Bool)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:253
│     [16] (::Pluto.var"#260#264"{Bool, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Pluto.ServerSession, Pluto.Notebook})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/evaluation/Run.jl:396
│     [17] withtoken(f::Pluto.var"#260#264"{Bool, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Pluto.ServerSession, Pluto.Notebook}, token::Pluto.Token)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/evaluation/Tokens.jl:19
│     [18] #259
│        @ ~/.julia/packages/Pluto/U4wvO/src/evaluation/Run.jl:395 [inlined]
│     [19] macro expansion
│        @ ~/.julia/packages/Pluto/U4wvO/src/evaluation/Tokens.jl:58 [inlined]
│     [20] (::Pluto.var"#252#253"{Pluto.var"#259#263"{Bool, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Pluto.ServerSession, Pluto.Notebook}})()
│        @ Pluto ./task.jl:484
└ @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:286
┌ Info: Backup saved to
└   backup_path = "/Users/cokes/intro_to_data_science_fall_2022/lectures/complete/working_with_data backup 4.jl"

version info

Pluto v0.19.13

julia> versioninfo()
Julia Version 1.8.2
Commit 36034abf260 (2022-09-29 15:21 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin21.3.0)
  CPU: 8 × Apple M1
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1)
  Threads: 1 on 4 virtual cores
@SimonEnsemble
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well, relaunching Pluto now opens the notebook and allows it run. but I get this error?

 LogLevel(1999): handle_connection handler error
│   exception =
│    Server never wrote a response
│    Stacktrace:
│     [1] error(s::String)
│       @ Base ./error.jl:35
│     [2] handle_connection(f::Function, c::HTTP.ConnectionPool.Connection, listener::HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, readtimeout::Int64, access_log::Nothing)
│       @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:445
│     [3] (::HTTP.Servers.var"#16#17"{Pluto.var"#396#406"{Pluto.ServerSession, HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing}}, HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, Set{HTTP.ConnectionPool.Connection}, Int64, Nothing, Base.Semaphore, HTTP.ConnectionPool.Connection})()
│       @ HTTP.Servers ./task.jl:484
└ @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:456
┌ LogLevel(1999): error while handling connection
│   exception =
│    IOError: write: broken pipe (EPIPE)
│    Stacktrace:
│     [1] uv_write(s::Sockets.TCPSocket, p::Ptr{UInt8}, n::UInt64)
│       @ Base ./stream.jl:1064
│     [2] unsafe_write(s::Sockets.TCPSocket, p::Ptr{UInt8}, n::UInt64)
│       @ Base ./stream.jl:1118
│     [3] unsafe_write(c::HTTP.ConnectionPool.Connection, p::Ptr{UInt8}, n::UInt64)
│       @ HTTP.ConnectionPool ~/.julia/packages/HTTP/fthyG/src/ConnectionPool.jl:105
│     [4] write(io::HTTP.ConnectionPool.Connection, s::String)
│       @ Base ./strings/io.jl:244
│     [5] write
│       @ ./io.jl:674 [inlined]
│     [6] unsafe_write(http::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.ConnectionPool.Connection}, p::Ptr{UInt8}, n::UInt64)
│       @ HTTP.Streams ~/.julia/packages/HTTP/fthyG/src/Streams.jl:96
│     [7] write(io::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.ConnectionPool.Connection}, s::String)
│       @ Base ./strings/io.jl:244
│     [8] handle_connection(f::Function, c::HTTP.ConnectionPool.Connection, listener::HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, readtimeout::Int64, access_log::Nothing)
│       @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:461
│     [9] (::HTTP.Servers.var"#16#17"{Pluto.var"#396#406"{Pluto.ServerSession, HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing}}, HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, Set{HTTP.ConnectionPool.Connection}, Int64, Nothing, Base.Semaphore, HTTP.ConnectionPool.Connection})()
│       @ HTTP.Servers ./task.jl:484
└ @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:473
┌ Info:
└ Opening http://localhost:1234/open?secret=wzYRw6uf&path=%2FUsers%2Fcokes%2Fintro_to_data_science_fall_2022%2Flectures%2Fcomplete%2Fworking_with_data.jl in your default browser... ~ have fun!
┌ Info:
│ Press Ctrl+C in this terminal to stop Pluto
└
    Updating registry at `~/.julia/registries/General`
    Updating ┌ LogLevel(1999): handle_connection handler error
│   exception =
│    SystemError: opening file "/Users/cokes/.julia/packages/Pluto/U4wvO/frontend-dist/logo.004c1d7c.svg": Too many open files
│    Stacktrace:
│      [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
│        @ Base ./error.jl:176
│      [2] #systemerror#80
│        @ ./error.jl:175 [inlined]
│      [3] systemerror
│        @ ./error.jl:175 [inlined]
│      [4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing)
│        @ Base ./iostream.jl:293
│      [5] open
│        @ ./iostream.jl:275 [inlined]
│      [6] open(f::Base.var"#385#386"{Tuple{}}, args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
│        @ Base ./io.jl:382
│      [7] open
│        @ ./io.jl:381 [inlined]
│      [8] read
│        @ ./io.jl:460 [inlined]
│      [9] asset_response(path::String; cacheable::Bool)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/webserver/Static.jl:54
│     [10] (::Pluto.var"#serve_asset#329")(request::HTTP.Messages.Request)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/webserver/Static.jl:422
│     [11] (::HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing})(req::HTTP.Messages.Request)
│        @ HTTP.Handlers ~/.julia/packages/HTTP/fthyG/src/Handlers.jl:439
│     [12] (::Pluto.var"#396#406"{Pluto.ServerSession, HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing}})(http::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.ConnectionPool.Connection})
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/webserver/WebServer.jl:249
│     [13] #invokelatest#2
│        @ ./essentials.jl:729 [inlined]
│     [14] invokelatest
│        @ ./essentials.jl:726 [inlined]
│     [15] handle_connection(f::Function, c::HTTP.ConnectionPool.Connection, listener::HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, readtimeout::Int64, access_log::Nothing)
│        @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:442
│     [16] (::HTTP.Servers.var"#16#17"{Pluto.var"#396#406"{Pluto.ServerSession, HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing}}, HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, Set{HTTP.ConnectionPool.Connection}, Int64, Nothing, Base.Semaphore, HTTP.ConnectionPool.Connection})()
│        @ HTTP.Servers ./task.jl:484
└ @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:456
┌ LogLevel(1999): handle_connection handler error
│   exception =
│    SystemError: opening file "/Users/cokes/.julia/packages/Pluto/U4wvO/frontend-dist/favicon_unsaturated.d1387b25.svg": Too many open files
│    Stacktrace:
│      [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
│        @ Base ./error.jl:176
│      [2] #systemerror#80
│        @ ./error.jl:175 [inlined]
│      [3] systemerror
│        @ ./error.jl:175 [inlined]
│      [4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing)
│        @ Base ./iostream.jl:293
│      [5] open
│        @ ./iostream.jl:275 [inlined]
│      [6] open(f::Base.var"#385#386"{Tuple{}}, args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
│        @ Base ./io.jl:382
│      [7] open
│        @ ./io.jl:381 [inlined]
│      [8] read
│        @ ./io.jl:460 [inlined]
│      [9] asset_response(path::String; cacheable::Bool)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/webserver/Static.jl:54
│     [10] (::Pluto.var"#serve_asset#329")(request::HTTP.Messages.Request)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/webserver/Static.jl:422
│     [11] (::HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing})(req::HTTP.Messages.Request)
│        @ HTTP.Handlers ~/.julia/packages/HTTP/fthyG/src/Handlers.jl:439
│     [12] (::Pluto.var"#396#406"{Pluto.ServerSession, HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing}})(http::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.ConnectionPool.Connection})
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/webserver/WebServer.jl:249
│     [13] #invokelatest#2
│        @ ./essentials.jl:729 [inlined]
│     [14] invokelatest
│        @ ./essentials.jl:726 [inlined]
│     [15] handle_connection(f::Function, c::HTTP.ConnectionPool.Connection, listener::HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, readtimeout::Int64, access_log::Nothing)
│        @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:442
│     [16] (::HTTP.Servers.var"#16#17"{Pluto.var"#396#406"{Pluto.ServerSession, HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing}}, HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, Set{HTTP.ConnectionPool.Connection}, Int64, Nothing, Base.Semaphore, HTTP.ConnectionPool.Connection})()
│        @ HTTP.Servers ./task.jl:484
└ @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:456
git-repo `https://github.com/JuliaRegistries/General`┌ LogLevel(1999): error while handling connection
│   exception =
│    IOError: write: broken pipe (EPIPE)
│    Stacktrace:
│     [1] uv_write(s::Sockets.TCPSocket, p::Ptr{UInt8}, n::UInt64)
│       @ Base ./stream.jl:1064
│     [2] unsafe_write(s::Sockets.TCPSocket, p::Ptr{UInt8}, n::UInt64)
│       @ Base ./stream.jl:1118
│     [3] unsafe_write(c::HTTP.ConnectionPool.Connection, p::Ptr{UInt8}, n::UInt64)
│       @ HTTP.ConnectionPool ~/.julia/packages/HTTP/fthyG/src/ConnectionPool.jl:105
│     [4] write(io::HTTP.ConnectionPool.Connection, s::String)
│       @ Base ./strings/io.jl:244
│     [5] write
│       @ ./io.jl:674 [inlined]
│     [6] unsafe_write(http::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.ConnectionPool.Connection}, p::Ptr{UInt8}, n::UInt64)
│       @ HTTP.Streams ~/.julia/packages/HTTP/fthyG/src/Streams.jl:96
│     [7] write(io::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.ConnectionPool.Connection}, s::String)
│       @ Base ./strings/io.jl:244
│     [8] handle_connection(f::Function, c::HTTP.ConnectionPool.Connection, listener::HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, readtimeout::Int64, access_log::Nothing)
│       @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:461
│     [9] (::HTTP.Servers.var"#16#17"{Pluto.var"#396#406"{Pluto.ServerSession, HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing}}, HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, Set{HTTP.ConnectionPool.Connection}, Int64, Nothing, Base.Semaphore, HTTP.ConnectionPool.Connection})()
│       @ HTTP.Servers ./task.jl:484
└ @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:473

┌ LogLevel(1999): error while handling connection
│   exception =
│    IOError: write: broken pipe (EPIPE)
│    Stacktrace:
│     [1] uv_write(s::Sockets.TCPSocket, p::Ptr{UInt8}, n::UInt64)
│       @ Base ./stream.jl:1064
│     [2] unsafe_write(s::Sockets.TCPSocket, p::Ptr{UInt8}, n::UInt64)
│       @ Base ./stream.jl:1118
│     [3] unsafe_write(c::HTTP.ConnectionPool.Connection, p::Ptr{UInt8}, n::UInt64)
│       @ HTTP.ConnectionPool ~/.julia/packages/HTTP/fthyG/src/ConnectionPool.jl:105
│     [4] write(io::HTTP.ConnectionPool.Connection, s::String)
│       @ Base ./strings/io.jl:244
│     [5] write
│       @ ./io.jl:674 [inlined]
│     [6] unsafe_write(http::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.ConnectionPool.Connection}, p::Ptr{UInt8}, n::UInt64)
│       @ HTTP.Streams ~/.julia/packages/HTTP/fthyG/src/Streams.jl:96
│     [7] write(io::HTTP.Streams.Stream{HTTP.Messages.Request, HTTP.ConnectionPool.Connection}, s::String)
│       @ Base ./strings/io.jl:244
│     [8] handle_connection(f::Function, c::HTTP.ConnectionPool.Connection, listener::HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, readtimeout::Int64, access_log::Nothing)
│       @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:461
│     [9] (::HTTP.Servers.var"#16#17"{Pluto.var"#396#406"{Pluto.ServerSession, HTTP.Handlers.Router{typeof(Pluto.default_404), typeof(HTTP.Handlers.default405), Nothing}}, HTTP.Servers.Listener{Nothing, Sockets.TCPServer}, Set{HTTP.ConnectionPool.Connection}, Int64, Nothing, Base.Semaphore, HTTP.ConnectionPool.Connection})()
│       @ HTTP.Servers ./task.jl:484
└ @ HTTP.Servers ~/.julia/packages/HTTP/fthyG/src/Servers.jl:473
┌ Error: Some registries failed to update:
│     — /Users/cokes/.julia/registries/General — failed to fetch from repo: failed to fetch from https://github.com/JuliaRegistries/General, error: GitError(Code:ERROR, Class:Net, failed to resolve address for github.com: nodename nor servname provided, or not known)
└ @ Pkg.Registry /Users/administrator/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-1.0/build/default-macmini-aarch64-1-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:449
┌ Warning: The project dependencies or compat requirements have changed since the manifest was last resolved.
│ It is recommended to `Pkg.resolve()` or consider `Pkg.update()` if necessary.
└ @ Pkg.API /Users/administrator/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-macmini-aarch64-1.0/build/default-macmini-aarch64-1-0/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Pkg/src/API.jl:1532

@SimonEnsemble
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ok this is now happening with all of my notebooks. weird. another error message below.

    Updating registry at `~/.julia/registries/General`
┌ Warning: PlutoPkg: Failed to add/remove packages! Resetting package environment...
│   PLUTO_VERSION = v"0.19.13"
│   VERSION = v"1.8.2"
│   old_packages =
│    11-element Vector{String}:
│     "CSV"
│     "Statistics"
│     ⋮
│     "DataFrames"
│   new_packages =
│    11-element Vector{String}:
│     "Statistics"
│     "StatsBase"
│     ⋮
│     "DataFrames"
│   exception =
│    GitError(Code:ENOTFOUND, Class:OS, failed to open directory '/Users/cokes/.julia/registries/General/': Too many open files)
│    Stacktrace:
│      [1] macro expansion
│        @ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/src/error.jl:110 [inlined]
│      [2] diff_tree(repo::LibGit2.GitRepo, tree::LibGit2.GitTree, pathspecs::String; cached::Bool)
│        @ LibGit2 /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/src/diff.jl:34
│      [3] isdiff(repo::LibGit2.GitRepo, treeish::String, paths::String; cached::Bool)
│        @ LibGit2 /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/src/LibGit2.jl:160
│      [4] #isdirty#101
│        @ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/src/LibGit2.jl:135 [inlined]
│      [5] isdirty (repeats 2 times)
│        @ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/src/LibGit2.jl:135 [inlined]
│      [6] (::Pkg.Registry.var"#59#63"{Base.TTY, Pkg.Registry.RegistryInstance, Vector{Tuple{String, String}}, String})(repo::LibGit2.GitRepo)
│        @ Pkg.Registry /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:402
│      [7] with(f::Pkg.Registry.var"#59#63"{Base.TTY, Pkg.Registry.RegistryInstance, Vector{Tuple{String, String}}, String}, obj::LibGit2.GitRepo)
│        @ LibGit2 /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/LibGit2/src/types.jl:1159
│      [8] update(regs::Vector{Pkg.Registry.RegistrySpec}; io::Base.TTY, force::Bool)
│        @ Pkg.Registry /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:401
│      [9] update(regs::Vector{Pkg.Registry.RegistrySpec}) (repeats 2 times)
│        @ Pkg.Registry /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:344
│     [10] update_registries(; force::Bool)
│        @ Pluto.PkgCompat ~/.julia/packages/Pluto/U4wvO/src/packages/PkgCompat.jl:169
│     [11] (::Pluto.var"#189#201"{Pluto.Notebook})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:202
│     [12] withio(f::Pluto.var"#189#201"{Pluto.Notebook}, ctx::Pkg.Types.Context, io::IOContext{IOBuffer})
│        @ Pluto.PkgCompat ~/.julia/packages/Pluto/U4wvO/src/packages/PkgCompat.jl:129
│     [13] (::Pluto.var"#182#193"{Pluto.Notebook, Pluto.IOListener, Vector{String}, Vector{String}, Bool, Bool})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:193
│     [14] withtoken(f::Pluto.var"#182#193"{Pluto.Notebook, Pluto.IOListener, Vector{String}, Vector{String}, Bool, Bool}, token::Pluto.Token)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/evaluation/Tokens.jl:19
│     [15] sync_nbpkg_core(notebook::Pluto.Notebook, old_topology::Pluto.NotebookTopology, new_topology::Pluto.NotebookTopology; on_terminal_output::Pluto.var"#iocallback#209"{Pluto.ServerSession, Pluto.Notebook}, lag::Float64)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:112
│     [16] (::Pluto.var"#206#208"{Pluto.ServerSession, Pluto.Notebook, Pluto.NotebookTopology, Pluto.NotebookTopology})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:262
│     [17] #205
│        @ ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:253 [inlined]
│     [18] sync_nbpkg(session::Pluto.ServerSession, notebook::Pluto.Notebook, old_topology::Pluto.NotebookTopology, new_topology::Pluto.NotebookTopology; save::Bool, take_token::Bool)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:253
│     [19] (::Pluto.var"#260#264"{Bool, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Pluto.ServerSession, Pluto.Notebook})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/evaluation/Run.jl:396
│     [20] withtoken(f::Pluto.var"#260#264"{Bool, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Pluto.ServerSession, Pluto.Notebook}, token::Pluto.Token)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/evaluation/Tokens.jl:19
│     [21] #259
│        @ ~/.julia/packages/Pluto/U4wvO/src/evaluation/Run.jl:395 [inlined]
│     [22] macro expansion
│        @ ~/.julia/packages/Pluto/U4wvO/src/evaluation/Tokens.jl:58 [inlined]
│     [23] (::Pluto.var"#252#253"{Pluto.var"#259#263"{Bool, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Pluto.ServerSession, Pluto.Notebook}})()
│        @ Pluto ./task.jl:484
└ @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:286
┌ Info: Backup saved to
└   backup_path = "/

then the next one after I restart is

┌ Warning: PlutoPkg: Failed to add/remove packages! Resetting package environment...
│   PLUTO_VERSION = v"0.19.13"
│   VERSION = v"1.8.2"
│   old_packages = String[]
│   new_packages =
│    11-element Vector{String}:
│     "Statistics"
│     "StatsBase"
│     ⋮
│     "DataFrames"
│   exception =
│    "/private/var/folders/mc/q4kv7qs121gc_0h42v317dyw0000gn/T/jl_7J0gDB/Project.toml": No such file
│    Stacktrace:
│      [1] error(::String, ::String)
│        @ Base ./error.jl:44
│      [2] readstring
│        @ /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/TOML/src/TOML.jl:21 [inlined]
│      [3] parsefile(f::String)
│        @ TOML /Applications/Julia-1.8.app/Contents/Resources/julia/share/julia/stdlib/v1.8/TOML/src/TOML.jl:43
│      [4] _modify_compat(f!::Pluto.PkgCompat.var"#27#28"{Pkg.Types.Context}, ctx::Pkg.Types.Context)
│        @ Pluto.PkgCompat ~/.julia/packages/Pluto/U4wvO/src/packages/PkgCompat.jl:408
│      [5] write_auto_compat_entries
│        @ ~/.julia/packages/Pluto/U4wvO/src/packages/PkgCompat.jl:430 [inlined]
│      [6] (::Pluto.var"#187#199"{Vector{String}, Pluto.Notebook, Pluto.IOListener})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:178
│      [7] withinteractive(f::Pluto.var"#187#199"{Vector{String}, Pluto.Notebook, Pluto.IOListener}, value::Bool)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:528
│      [8] #186
│        @ ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:150 [inlined]
│      [9] withio(f::Pluto.var"#186#198"{Vector{String}, Pluto.Notebook, Pluto.IOListener}, ctx::Pkg.Types.Context, io::IOContext{IOBuffer})
│        @ Pluto.PkgCompat ~/.julia/packages/Pluto/U4wvO/src/packages/PkgCompat.jl:129
│     [10] (::Pluto.var"#182#193"{Pluto.Notebook, Pluto.IOListener, Vector{String}, Vector{String}, Bool, Bool})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:149
│     [11] withtoken(f::Pluto.var"#182#193"{Pluto.Notebook, Pluto.IOListener, Vector{String}, Vector{String}, Bool, Bool}, token::Pluto.Token)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/evaluation/Tokens.jl:19
│     [12] sync_nbpkg_core(notebook::Pluto.Notebook, old_topology::Pluto.NotebookTopology, new_topology::Pluto.NotebookTopology; on_terminal_output::Pluto.var"#iocallback#209"{Pluto.ServerSession, Pluto.Notebook}, lag::Float64)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:112
│     [13] (::Pluto.var"#206#208"{Pluto.ServerSession, Pluto.Notebook, Pluto.NotebookTopology, Pluto.NotebookTopology})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:262
│     [14] #205
│        @ ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:253 [inlined]
│     [15] sync_nbpkg(session::Pluto.ServerSession, notebook::Pluto.Notebook, old_topology::Pluto.NotebookTopology, new_topology::Pluto.NotebookTopology; save::Bool, take_token::Bool)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:253
│     [16] (::Pluto.var"#260#264"{Bool, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Pluto.ServerSession, Pluto.Notebook})()
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/evaluation/Run.jl:396
│     [17] withtoken(f::Pluto.var"#260#264"{Bool, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Pluto.ServerSession, Pluto.Notebook}, token::Pluto.Token)
│        @ Pluto ~/.julia/packages/Pluto/U4wvO/src/evaluation/Tokens.jl:19
│     [18] #259
│        @ ~/.julia/packages/Pluto/U4wvO/src/evaluation/Run.jl:395 [inlined]
│     [19] macro expansion
│        @ ~/.julia/packages/Pluto/U4wvO/src/evaluation/Tokens.jl:58 [inlined]
│     [20] (::Pluto.var"#252#253"{Pluto.var"#259#263"{Bool, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, Pluto.ServerSession, Pluto.Notebook}})()
│        @ Pluto ./task.jl:484
└ @ Pluto ~/.julia/packages/Pluto/U4wvO/src/packages/Packages.jl:286

@SimonEnsemble
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if this happens to anyone else, 🥳 resolved by deleting ~/.julia/registries/General!

@fonsp fonsp self-assigned this Oct 13, 2022
@fonsp fonsp added the package manager Pluto's built-in package manager label Oct 13, 2022
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fonsp commented Oct 17, 2022

Thanks @SimonEnsemble !

I have seen other issues related to the registry folder getting "corrupted" in the past, but this problem should start to get resolved by the move to a tarball registry in Julia 1.6 (JuliaLang/Pkg.jl#2017 (comment)).

The logs in this issue happened in the finally block after the actual error, where Pkg.add failed because of a corrupt registry. I fixed the error in the logs in 9aad08d , but unfortunately there are no logs about the underlying issue.

After the fix of 9aad08d , we will be able to get a better error message when this happens again, but it seems like this issue will be too difficult to reproduce, so I will close this for now.

@fonsp fonsp closed this as completed Oct 17, 2022
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fonsp commented Oct 17, 2022

@SimonEnsemble Do you remember setting up the General registry manually? Is it possible that you were using a git registry instead of a tarball registry? JuliaLang/Pkg.jl#2431

@SimonEnsemble
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👁️
at one point I had compiled Julia from the master branch to get it to work on my M1 silicon.
other than this information, I don't recall ever doing anything manual with the General registry.

thanks!

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