SystemError: opening file "C:\\Users\\justi\\.julia\\registries\\General\\Registry.toml": No such file or directory #1667

justintong97 · 2020-02-12T04:46:43Z

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When i type Pkg.add("IJulia")
it returns: SystemError: opening file "C:\Users\justi\.julia\registries\General\Registry.toml": No such file or directory

Thanks for contributing to the Julia project!

The text was updated successfully, but these errors were encountered:

fredrikekre · 2020-02-12T07:11:49Z

Can you try to delete C:\Users\justi\.julia\registries\General and try again?

justintong97 · 2020-02-12T16:37:51Z

it works， thanks for solving my problem 获取 Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ 发件人: Fredrik Ekre <[email protected]> 发送时间: Wednesday, February 12, 2020 1:11:49 AM 收件人: JuliaLang/Pkg.jl <[email protected]> 抄送: Tong, Jiacheng <[email protected]>; Author <[email protected]> 主题: [External] Re: [JuliaLang/Pkg.jl] SystemError: opening file "C:\\Users\\justi\\.julia\\registries\\General\\Registry.toml": No such file or directory (#1667) Can you try to delete C:\Users\justi\.julia\registries\General and try again? ― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#1667?email_source=notifications&email_token=AI64ZNYUEB42DY7RGAOD4E3RCOOLLA5CNFSM4KTT5VUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELPVZ5Y#issuecomment-585063671>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AI64ZN5LGJJ23V47ENVPOITRCOOLLANCNFSM4KTT5VUA>.

00vareladavid · 2020-02-12T16:42:15Z

Perhaps we can detect this ourselves and re-download General if this is the case?

AndyAbok · 2020-05-29T06:16:08Z

Can you try to delete C:\Users\justi\.julia\registries\General and try again?

when you say delete how do you mean facing the same issue over here when tried to add the general after removing it since DataFrames was having issues with versioning

julia> Pkg.Registry.add("General")
Cloning registry from "https://github.com/JuliaRegistries/General.git"
ERROR: SystemError: opening file "C:\Users\andrewa\.julia\registries\General\Registry.toml": No such file or directory
Stacktrace:
[1] systemerror(::String, ::Int32; extrainfo::Nothing) at .\error.jl:168
[2] #systemerror#50 at .\error.jl:167 [inlined]
[3] systemerror at .\error.jl:167 [inlined]
[4] open(::String; read::Bool, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing) at .\iostream.jl:254
[5] open(::String, ::String) at .\iostream.jl:310
[6] open(::typeof(Pkg.TOML.parse), ::String, ::Vararg{String,N} where N; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at .\io.jl:296
[7] open at .\io.jl:296 [inlined]
[8] parsefile at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\ext\TOML\src\TOML.jl:50 [inlined]
[9] read_registry(::String; cache::Bool) at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Types.jl:974
[10] read_registry at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Types.jl:969 [inlined]
[11] (::Pkg.Types.var"#92#95"{Pkg.Types.Context,String,Pkg.Types.RegistrySpec})(::String) at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Types.jl:946
[12] mktempdir(::Pkg.Types.var"#92#95"{Pkg.Types.Context,String,Pkg.Types.RegistrySpec}, ::String; prefix::String) at .\file.jl:682
[13] mktempdir at .\file.jl:680 [inlined] (repeats 2 times)
[14] clone_or_cp_registries(::Pkg.Types.Context, ::Array{Pkg.Types.RegistrySpec,1}, ::String) at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Types.jl:911
[15] clone_or_cp_registries at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Types.jl:905 [inlined]
[16] #add#6 at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Registry.jl:29 [inlined]
[17] add at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Registry.jl:28 [inlined]
[18] #add#5 at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Registry.jl:26 [inlined]
[19] add at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Registry.jl:26 [inlined]
[20] add(::Array{String,1}; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Registry.jl:25
[21] add at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Registry.jl:25 [inlined]
[22] #add#1 at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Registry.jl:24 [inlined]
[23] add(::String) at D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Registry.jl:24
[24] top-level scope at REPL[173]:1

Alexander-Barth · 2020-09-24T13:40:53Z

I see this error too from time to time on Windows computers (last time on a Windows computer with julia 1.5.1 from a student). Removing C:\Users\<name>\.julia\registries\General always resolved the problem, but it would be nice to know the root cause of it. Unfortunately, this issue is very difficult to reproduce.

Here are other reports:
https://discourse.julialang.org/t/unable-to-install-ijulia/47160/2
JuliaLang/julia#37521

Is there any information that would be helpful to collect the next time this issue shows up? Maybe Linux and Mac handle better transient network issues when doing a git checkout than Windows?

fredrikekre · 2020-09-24T14:24:19Z

it would be nice to know the root cause of it.

Windows or some program on your computer deletes it.

fredrikekre · 2020-09-24T14:25:35Z

Here is another example where Windows deleted folders even: #2017 (comment), and here are a bunch more https://discourse.julialang.org/search?q=Registry.toml%22%3A%20No%20such%20file%20or%20directory

StefanKarpinski · 2020-09-25T22:26:54Z

It's absolutely bananas that Windows just deletes stuff, but that seems to be what happens.

Alexander-Barth · 2020-09-29T07:52:30Z

Yesterday, I had the first time seen this error (/Users/admin/.julia/registries/General/Registry.toml": No such file or directory while installing the first julia package; julia 1.5.1, I think) on a student's Mac. I thought that this problem was Windows specific.

I had a look at the code, and it is really strange:

At line 1004 the file is there (as the error message is not printed),

Pkg.jl/src/Types.jl

Line 1004 in f1430b5

if !isfile(joinpath(tmp, "Registry.toml"))
At line 1007, Registry.toml is missing

Pkg.jl/src/Types.jl

Line 1007 in f1430b5

registry = read_registry(joinpath(tmp, "Registry.toml"); cache=false) # don't cache this tmp registry

fredrikekre · 2020-09-29T08:13:42Z

The error is from a later stage after the registry has been copied to the correct place.

j-fu · 2020-11-12T23:26:00Z

Hi, such things seem to happen also outside of Julia...

https://www.tenforums.com/general-support/121122-empty-folders-disappearing.html
https://www.tenforums.com/general-support/121891-downloads-folder-windows-10-1809-a.html
https://techcommunity.microsoft.com/t5/storage-at-microsoft/windows-10-and-storage-sense/ba-p/428270

There seems to be a thing like StorageSense which may be involved. Also some people report about
deactivating AV software like avast. No clear picture though.

Disclaimer: I am not a windows user, just do it occasionally in a VM - for the odd .docx and for testing Julia packges, so all of this was just googled.

fonsp · 2020-11-13T00:23:31Z

I hear about this problem very often from new Pluto users. I think the most common cause is:

Do a pkg> command
It starts updating the registry without a progress bar
After X minutes, I assume that something is broken and I Ctrl+C

The result is either this issue, or an incomplete registry ("package not found" errors) - both have unhelpful error messages.

But using the tarball directly in future Pkg version will also solve this issue, right?

j-fu · 2020-11-13T08:41:02Z

So it seems that there are possibly two problems here: windows possibly deleting files, and slow communication regarding packages. @fonsp: did you experiment with switching of the package server comunication by unsetting JULIA_PKG_SERVER ?

EDIT: May be also related to #2175 - it seems that the default for windows is being reset to git cloning.

musm · 2020-12-04T19:38:59Z

I'm also getting this

SimonEnsemble · 2020-12-07T04:05:18Z

one of my students got this error on Mac:

SystemError: opening file "/Users/sarahutton/.julia/registries/General/Registry.toml": No such file or directory

Manas2030 · 2021-01-18T07:32:14Z

Hi, I got the same error message even though I had my StorageSense turned off. But I was able to succesfully run the Pkg.add() command after adding, the "/.julia/registries/General" folder to my windows defender exclusions.

SimonEnsemble · 2021-01-18T18:46:09Z

to give an idea of prevalence: in my class of 86, ~6 students had this problem, where they needed to delete the General folder.

IanButterworth · 2021-01-20T02:55:48Z

Is what's happening here something like this?

User initializes the registry, either by their first pkg> add or explicitly pkg> registry add
Sees things going slowly so ctrl-c's, which may occur during the cp here (which is a mv on more recent julia)

Pkg.jl/src/Types.jl

Line 1027 in aaf4e6e

cp(tmp, regpath)
The cp didn't get as far as copying Registry.toml over, which on windows happens alphabetically after the R dir has copied
The user tries again to add etc.
The logic here checks that the registry dir exists but not the Registry.toml file specifically

Pkg.jl/src/Types.jl

Line 1015 in aaf4e6e

if Pkg.isdir_nothrow(regpath)
Goes on to open the nonexistent Registry.toml file

Full section (this is from Pkg that shipped with 1.5.1 so I could line up with the trace in https://discourse.julialang.org/t/unable-to-install-ijulia/47160)

Pkg.jl/src/Types.jl

Lines 1013 to 1029 in aaf4e6e

    
           regpath = joinpath(depot, "registries", registry["name"]#=, slug=#) 
        
           ispath(dirname(regpath)) || mkpath(dirname(regpath)) 
        
           if Pkg.isdir_nothrow(regpath) 
        
               existing_registry = read_registry(joinpath(regpath, "Registry.toml")) 
        
               if registry["uuid"] == existing_registry["uuid"] 
        
                   println(ctx.io, 
        
                           "registry `$(registry["name"])` already exist in `$(Base.contractuser(regpath))`.") 
        
               else 
        
                   throw(PkgError("registry `$(registry["name"])=\"$(registry["uuid"])\"` conflicts with " * 
        
                       "existing registry `$(existing_registry["name"])=\"$(existing_registry["uuid"])\"`. " * 
        
                       "To install it you can clone it manually into e.g. " * 
        
                       "`$(Base.contractuser(joinpath(depot, "registries", registry["name"]*"-2")))`.")) 
        
               end 
        
           else 
        
               cp(tmp, regpath) 
        
               printpkgstyle(ctx, :Added, "registry `$(registry["name"])` to `$(Base.contractuser(regpath))`") 
        
           end

If that is what's happening, this might be a fix: #2349

IanButterworth · 2021-01-20T07:17:07Z

This appears to be fixed in 1.6 already, by changing from cp-ing to mv-ing the registry from temp

Rapsodia86 · 2021-01-21T19:15:07Z

Just to let you all know, It is not only Windows/Mac issue. I just had it on Linux as well.

StefanKarpinski · 2021-01-21T19:25:04Z

That supports the theory that it's the cp being slow and getting interrupted half way through since that isn't Windows-specific (although it's worse on Windows since file operations are so slow there).

IanButterworth · 2021-01-23T17:23:05Z

Nightly will still do this if a registry dir is present but missing a Registry.toml, which may happen if people use older and newer julia versions together.
This might be a better check to make #2356

Flourish38 · 2021-01-24T09:24:32Z

This also happened to me after Ctrl-C on a pkg> add command, I'm on Windows. Seems you all pretty much have it figured out, and the workaround isn't so bad in the meantime. Thanks for the help!

bughht · 2021-01-27T15:45:16Z

The issue also happened to me after I shut down installing packages, deleting the General folder actually works for me, thanks.

fredrikekre · 2021-01-27T15:48:30Z

Likely fixed by #2356

sudhakar086 · 2021-02-11T02:35:51Z

Can you try to delete C:\Users\justi\.julia\registries\General and try again?

wonderfull

cveintimillat · 2021-02-14T12:19:23Z

Can you try to delete C:\Users\justi\.julia\registries\General and try again?

This did the trick

Republic1024 · 2021-08-17T12:08:54Z

Can you try to delete C:\Users\justi\.julia\registries\General and try again?

May be function

ron-wolf · 2023-09-15T20:04:53Z

Hello all, I think I am just now seeing this issue crop up in September 2023. I am using Julia 1.9.2 on Windows 10, build 19045.3448. I am also a Pluto user. Anything I can do to help reproduce this?

KristofferC transferred this issue from JuliaLang/julia Feb 12, 2020

KristofferC mentioned this issue Oct 1, 2020

First run of Julia can result in corrupt state JuliaLang/julia#37833

Closed

fredrikekre mentioned this issue Oct 7, 2020

I can't install IJulia JuliaLang/IJulia.jl#952

Closed

Plecra mentioned this issue Nov 12, 2020

Pkg.jl will corrupt itself on Windows fonsp/Pluto.jl#671

Closed

IanButterworth mentioned this issue Jan 20, 2021

Registry: Change update from cp to mv #2349

Merged

IanButterworth mentioned this issue Jan 23, 2021

Registry add: Overwrite registry folders that don't contain a Registry.toml #2356

Merged

fredrikekre closed this as completed Jan 27, 2021

IanButterworth mentioned this issue Feb 13, 2021

No such directory #2392

Closed

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SystemError: opening file "C:\\Users\\justi\\.julia\\registries\\General\\Registry.toml": No such file or directory #1667

SystemError: opening file "C:\\Users\\justi\\.julia\\registries\\General\\Registry.toml": No such file or directory #1667

justintong97 commented Feb 12, 2020

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SystemError: opening file "C:\\Users\\justi\\.julia\\registries\\General\\Registry.toml": No such file or directory #1667

SystemError: opening file "C:\\Users\\justi\\.julia\\registries\\General\\Registry.toml": No such file or directory #1667

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