Running a notebook deleted contents of .julia/registries

[KronosTheLate]

WARNING - the post has been rewritten. It currently does not seem like the pluto notebook process is the culprit, but a trigger event that can cause the bug. Updated info below. Closing this for now, as it does not seem appropriate here

The problem is that during what I have identified as "trigger events", the contents of my .julia/registries folder is deleted. This can occur when I

1. update or install packages (specifically during the "Updating registry at C:\Users\username.julia\registries\General" step)
2. Run a pluto notebook. The notebook can be empty or contain a single cell with 1+1 and the problem can occur. When the error occurs, the notebook is not responsive, and a result is never evaluated, nor does the cell timer count.

The deletion of the folder contents happen during the Updating registry step, or the notebook has appear to run for about a minute. The behaviour is not consistently reproduced, but it is reoccuring. Package updating and installing has been a trigger event at least 3 times, and the notebook process has been a trigger event about 10 times. The problem can be consistent, then be fixed for time time, but then reoccur again soon.

Below is the error thrown upon stopping a not-responding pluto-notebook:

┌ Error: mktempdir cleanup
│   exception =
│    InterruptException:
│    Stacktrace:
│     [1] unlink(::String) at .\file.jl:917
│     [2] rm(::String; force::Bool, recursive::Bool) at .\file.jl:268
│     [3] rm(::String; force::Bool, recursive::Bool) at .\file.jl:278 (repeats 3 times)
│     [4] mktempdir(::Pkg.Types.var"#107#110"{String}, ::String; prefix::String) at .\file.jl:714
│     [5] mktempdir(::Function, ::String) at .\file.jl:707 (repeats 2 times)
│     [6] update_registries(::Pkg.Types.Context, ::Array{Pkg.Types.RegistrySpec,1}; force::Bool) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\Types.jl:1119
│     [7] up(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; level::Pkg.Types.UpgradeLevel, mode::Pkg.Types.PackageMode, update_registry::Bool, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:227
│     [8] #up#38 at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:68 [inlined]
│     [9] instantiate(::Pkg.Types.Context; manifest::Nothing, update_registry::Bool, verbose::Bool, platform::Pkg.BinaryPlatforms.Windows, kwargs::Base.Iterators.Pairs{Symbol,Base.DevNull,Tuple{Symbol},NamedTuple{(:io,),Tuple{Base.DevNull}}}) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Pkg\src\API.jl:810
│     [10] top-level scope at C:\Users\densb\.julia\packages\Pluto\luIaC\src\runner\Loader.jl:19
│     [11] include(::String) at .\client.jl:457
│     [12] top-level scope at none:1
│     [13] eval(::Module, ::Any) at .\boot.jl:331
│     [14] (::Distributed.var"#103#104"{Distributed.CallMsg{:call}})() at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Distributed\src\process_messages.jl:290
│     [15] run_work_thunk(::Distributed.var"#103#104"{Distributed.CallMsg{:call}}, ::Bool) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Distributed\src\process_messages.jl:79
│     [16] run_work_thunk(::Distributed.RemoteValue, ::Function) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Distributed\src\process_messages.jl:88
│     [17] (::Distributed.var"#96#98"{Distributed.RemoteValue,Distributed.var"#103#104"{Distributed.CallMsg{:call}}})() at .\task.jl:356
└ @ Base.Filesystem file.jl:717
TaskFailedException:
InterruptException:
Stacktrace:
 [1] sync_end(::Channel{Any}) at .\task.jl:314
 [2] macro expansion at .\task.jl:333 [inlined]
 [3] remotecall_eval(::Module, ::Array{Int64,1}, ::Expr) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Distributed\src\macros.jl:218
 [4] create_workspaceprocess(; compiler_options::Pluto.Configuration.CompilerOptions) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\WorkspaceManager.jl:170
 [5] make_workspace(::Tuple{Pluto.ServerSession,Pluto.Notebook}) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\WorkspaceManager.jl:43
 [6] #7 at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\WorkspaceManager.jl:188 [inlined]
 [7] macro expansion at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\Tokens.jl:76 [inlined]
 [8] (::Pluto.var"#1#2"{Pluto.WorkspaceManager.var"#7#9"{Tuple{Pluto.ServerSession,Pluto.Notebook}},Pluto.Promise{Pluto.WorkspaceManager.Workspace}})() at .\task.jl:356┌ Warning: Response function to message of type complete failed
└ @ Pluto C:\Users\densb\.julia\packages\Pluto\luIaC\src\webserver\WebServer.jl:359

Stacktrace:┌ Warning: Reading WebSocket client stream failed for unknown reason:
│   parentbody =
│    Dict{Any,Any} with 5 entries:
│      "client_id"   => "1wwwjfk"
│      "body"        => Dict{Any,Any}("query"=>"sq")
│      "request_id"  => "bkboqy"
│      "notebook_id" => "03f35370-5341-11eb-0379-49c494b1da65"
│      "type"        => "complete"
│   exception =
│    TaskFailedException:
│    InterruptException:
│    Stacktrace:
│     [1] sync_end(::Channel{Any}) at .\task.jl:314
│     [2] macro expansion at .\task.jl:333 [inlined]
│     [3] remotecall_eval(::Module, ::Array{Int64,1}, ::Expr) at C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.5\Distributed\src\macros.jl:218
│     [4] create_workspaceprocess(; compiler_options::Pluto.Configuration.CompilerOptions) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\WorkspaceManager.jl:170
│     [5] make_workspace(::Tuple{Pluto.ServerSession,Pluto.Notebook}) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\WorkspaceManager.jl:43
│     [6] #7 at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\WorkspaceManager.jl:188 [inlined]
│     [7] macro expansion at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\Tokens.jl:76 [inlined]
│     [8] (::Pluto.var"#1#2"{Pluto.WorkspaceManager.var"#7#9"{Tuple{Pluto.ServerSession,Pluto.Notebook}},Pluto.Promise{Pluto.WorkspaceManager.Workspace}})() at .\task.jl:356
│    Stacktrace:
│     [1] wait at .\task.jl:267 [inlined]
│     [2] wait(::Pluto.Promise{Pluto.WorkspaceManager.Workspace}) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\Tokens.jl:83
│     [3] get_workspace at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\WorkspaceManager.jl:190 [inlined]
│     [4] (::Pluto.var"#201#203")(::Pluto.ServerSession, ::Dict{Any,Any}, ::Pluto.Notebook; initiator::Pluto.Initiator) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\webserver\REPLTools.jl:60
│     [5] process_ws_message(::Pluto.ServerSession, ::Dict{Any,Any}, ::HTTP.WebSockets.WebSocket{HTTP.ConnectionPool.Transaction{Sockets.TCPSocket}}) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\webserver\WebServer.jl:357
│     [6] (::Pluto.var"#215#225"{Pluto.ServerSession,Base.RefValue{Function}})(::HTTP.WebSockets.WebSocket{HTTP.ConnectionPool.Transaction{Sockets.TCPSocket}}) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\webserver\WebServer.jl:160
│     [7] upgrade(::Pluto.var"#215#225"{Pluto.ServerSession,Base.RefValue{Function}}, ::HTTP.Streams.Stream{HTTP.Messages.Request,HTTP.ConnectionPool.Transaction{Sockets.TCPSocket}}; binary::Bool) at C:\Users\densb\.julia\packages\HTTP\IAI92\src\WebSockets.jl:160
│     [8] upgrade at C:\Users\densb\.julia\packages\HTTP\IAI92\src\WebSockets.jl:142 [inlined]
│     [9] (::Pluto.var"#214#224"{Pluto.ServerSession,HTTP.Handlers.Router{Symbol("##253")},Base.RefValue{Function}})(::HTTP.Streams.Stream{HTTP.Messages.Request,HTTP.ConnectionPool.Transaction{Sockets.TCPSocket}}) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\webserver\WebServer.jl:147
│     [10] handle at C:\Users\densb\.julia\packages\HTTP\IAI92\src\Handlers.jl:269 [inlined]
│     [11] #4 at C:\Users\densb\.julia\packages\HTTP\IAI92\src\Handlers.jl:345 [inlined]
│     [12] macro expansion at C:\Users\densb\.julia\packages\HTTP\IAI92\src\Servers.jl:367 [inlined]
│     [13] (::HTTP.Servers.var"#13#14"{HTTP.Handlers.var"#4#5"{HTTP.Handlers.StreamHandlerFunction{Pluto.var"#214#224"{Pluto.ServerSession,HTTP.Handlers.Router{Symbol("##253")},Base.RefValue{Function}}}},HTTP.ConnectionPool.Transaction{Sockets.TCPSocket},HTTP.Streams.Stream{HTTP.Messages.Request,HTTP.ConnectionPool.Transaction{Sockets.TCPSocket}}})() at .\task.jl:356
└ @ Pluto C:\Users\densb\.julia\packages\Pluto\luIaC\src\webserver\WebServer.jl:168

 [1] wait at .\task.jl:267 [inlined]
 [2] wait(::Pluto.Promise{Pluto.WorkspaceManager.Workspace}) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\Tokens.jl:83
 [3] get_workspace at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\WorkspaceManager.jl:190 [inlined]
 [4] delete_vars(::Tuple{Pluto.ServerSession,Pluto.Notebook}, ::Set{Symbol}, ::Set{Tuple{Base.UUID,Array{Symbol,1}}}, ::Set{Expr}; kwargs::Base.Iterators.Pairs{Symbol,Array{Pluto.Cell,1},Tuple{Symbol},NamedTuple{(:to_run,),Tuple{Array{Pluto.Cell,1}}}}) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\WorkspaceManager.jl:273
 [5] run_reactive!(::Pluto.ServerSession, ::Pluto.Notebook, ::Pluto.NotebookTopology, ::Pluto.NotebookTopology, ::Array{Pluto.Cell,1}; deletion_hook::Function, persist_js_state::Bool) at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\Run.jl:65
 [6] run_reactive! at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\Run.jl:26 [inlined]
 [7] macro expansion at C:\Users\densb\.julia\packages\Pluto\luIaC\src\evaluation\Run.jl:13 [inlined]
 [8] (::Pluto.var"#79#81"{Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}},Pluto.ServerSession,Pluto.Notebook,Pluto.NotebookTopology,Pluto.NotebookTopology,Array{Pluto.Cell,1}})() at .\task.jl:356

At some point yesterday, the notebook started working consistently, but gave the following error message every time I stopped the process:

┌ Warning: temp cleanup
│   exception =
│    schedule: Task not runnable
│    Stacktrace:
│     [1] error(::String) at .\error.jl:33
│     [2] enq_work(::Task) at .\task.jl:526
│     [3] yield at .\task.jl:626 [inlined]
│     [4] yield at .\task.jl:625 [inlined]
│     [5] Channel{Any}(::Base.Filesystem.var"#_it#24"{Bool,Bool,typeof(throw),String,Array{String,1},Array{String,1}}, ::Int64; taskref::Nothing, spawn::Bool) at .\channels.jl:135
│     [6] #Channel#488 at .\channels.jl:157 [inlined]
│     [7] Channel at .\channels.jl:150 [inlined]
│     [8] walkdir(::String; topdown::Bool, follow_symlinks::Bool, onerror::typeof(throw)) at .\file.jl:913
│     [9] walkdir at .\file.jl:872 [inlined]
│     [10] prepare_for_deletion(::String) at .\file.jl:478
│     [11] temp_cleanup_purge(::Bool) at .\file.jl:513
│     [12] temp_cleanup_purge() at .\file.jl:507
│     [13] _atexit() at .\initdefs.jl:316
└ @ Base.Filesystem file.jl:518
      From worker 2:    InterruptException()