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ERROR: GitError(Code:EMERGECONFLICT, Class:Checkout, 492 conflicts prevent checkout) #1161

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nbakas opened this issue Apr 17, 2019 · 10 comments
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ERROR: GitError(Code:EMERGECONFLICT, Class:Checkout, 492 conflicts prevent checkout) #1161

nbakas opened this issue Apr 17, 2019 · 10 comments

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@nbakas
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nbakas commented Apr 17, 2019

When I try to add any new package or do Pkg.update()
Julia version 1.0.3.1 on Windows 10
@StefanKarpinski
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It sounds like you may have a dev'd repo that is in a conflicting state and cannot be updated.

@KristofferC
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Dev'd repos are never updated though.

More information are needed to answer this. Output of Pkg.status(). Does it happen in an empty project? Etc.

@StefanKarpinski
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I guess it's possible that the registry repo is in a messed up state. If that's the case, the fix is:
a) don't manually mess with the registry repos or, if you do then fix them before trying to update
b) for this time, go into ~/.julia/registries/General/ and make sure you're ok with blowing away whatever is in there and if you are then you can just delete that entire directory.

@nbakas
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nbakas commented Apr 17, 2019 •
edited by KristofferC

Thanks for the immediate replies!

It happens in an empty project, I just start Julia (in Atom/Juno)

Status `C:\Users\...\.juliapro\JuliaPro_v1.0.3.1\environments\v1.0\Project.toml`
  [e5e0dc1b] Juno v0.5.3

In ~/.juliapro/registries/ here is no folder General
note: I have ~/.juliapro and ~/.julia as well, I suppose the second remained from older installations

Here is the complete message

GitError(Code:EMERGECONFLICT, Class:Checkout, 492 conflicts prevent checkout)
macro expansion at error.jl:101 [inlined]
#checkout_tree#46(::LibGit2.CheckoutOptions, ::Function, ::LibGit2.GitRepo, ::LibGit2.GitCommit) at repository.jl:358
checkout_tree at repository.jl:356 [inlined]
ffmerge!(::LibGit2.GitRepo, ::LibGit2.GitAnnotated) at merge.jl:107
#merge!#89(::LibGit2.MergeOptions, ::LibGit2.CheckoutOptions, ::Function, ::LibGit2.GitRepo, ::Array{LibGit2.GitAnnotated,1}, ::Bool) at merge.jl:234
#merge! at none:0 [inlined]
#merge!#140(::String, ::String, ::Bool, ::LibGit2.MergeOptions, ::LibGit2.CheckoutOptions, ::Function, ::LibGit2.GitRepo) at LibGit2.jl:784
#merge! at none:0 [inlined]
update_registries(::Pkg.Types.Context, ::Array{Pkg.Types.RegistrySpec,1}) at Types.jl:1254
update_registries at Types.jl:1219 [inlined]
#handle_repos_add!#61(::Bool, ::Nothing, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at Types.jl:719
#handle_repos_add! at API.jl:0 [inlined]
#add_or_develop#15(::Symbol, ::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at API.jl:42
#add_or_develop at none:0 [inlined]
#add_or_develop#14 at API.jl:31 [inlined]
#add_or_develop at none:0 [inlined]
#add_or_develop#13 at API.jl:29 [inlined]
#add_or_develop at none:0 [inlined]
#add_or_develop#12 at API.jl:28 [inlined]
#add_or_develop at none:0 [inlined]
#add#20 at API.jl:59 [inlined]
add(::String) at API.jl:59
top-level scope at none:0
include_string(::Module, ::String, ::String) at loading.jl:1008
include_string(::Module, ::String, ::String, ::Int64) at eval.jl:30
(::getfield(Atom, Symbol("##114#119")){String,Int64,String})() at eval.jl:94
withpath(::getfield(Atom, Symbol("##114#119")){String,Int64,String}, ::Nothing) at utils.jl:30
withpath at eval.jl:46 [inlined]
#113 at eval.jl:93 [inlined]
with_logstate(::getfield(Atom, Symbol("##113#118")){String,Int64,String}, ::Base.CoreLogging.LogState) at logging.jl:395
with_logger at logging.jl:491 [inlined]
#112 at eval.jl:92 [inlined]
hideprompt(::getfield(Atom, Symbol("##112#117")){String,Int64,String}) at repl.jl:85
macro expansion at eval.jl:91 [inlined]
(::getfield(Atom, Symbol("##111#116")))(::Dict{String,Any}) at eval.jl:86
handlemsg(::Dict{String,Any}, ::Dict{String,Any}) at comm.jl:164
(::getfield(Atom, Symbol("##19#21")){Array{Any,1}})() at task.jl:259

@KristofferC
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Could you try remove the julia pro registry (just remove the directory in .juliapro/registries

@nbakas
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nbakas commented Apr 17, 2019

I deleted folder registries, then restarted Julia, I got a message

Hold on tight while we're installing some packages for you.
This should only take a few seconds...

Updating registry at C:\Users\...\.juliapro\JuliaPro_v1.0.3.1\registries\JuliaPro
Updating

[2] #checkout_tree#46(::LibGit2.CheckoutOptions, ::Function, ::LibGit2.GitRepo, ::LibGit2.GitCommit) at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\LibGit2\src\repository.jl:358
[3] checkout_tree at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\LibGit2\src\repository.jl:356 [inlined]
[4] ffmerge!(::LibGit2.GitRepo, ::LibGit2.GitAnnotated) at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\LibGit2\src\merge.jl:107
[5] #merge!#89(::LibGit2.MergeOptions, ::LibGit2.CheckoutOptions, ::Function, ::LibGit2.GitRepo, ::Array{LibGit2.GitAnnotated,1}, ::Bool) at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\LibGit2\src\merge.jl:234
[6] #merge! at .\none:0 [inlined]
[7] #merge!#140(::String, ::String, ::Bool, ::LibGit2.MergeOptions, ::LibGit2.CheckoutOptions, ::Function, ::LibGit2.GitRepo) at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\LibGit2\src\LibGit2.jl:784
[8] #merge! at .\none:0 [inlined]
[9] update_registries(::Pkg.Types.Context, ::Array{Pkg.Types.RegistrySpec,1}) at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\Pkg\src\Types.jl:1254
[10] update_registries at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\Pkg\src\Types.jl:1219 [inlined]
[11] #handle_repos_add!#61(::Bool, ::Nothing, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\Pkg\src\Types.jl:719
[12] #handle_repos_add! at .\none:0 [inlined]
[13] #add_or_develop#15(::Symbol, ::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1})
at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\Pkg\src\API.jl:42
[14] #add_or_develop at .\none:0 [inlined]
[15] #add_or_develop#14 at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\Pkg\src\API.jl:31 [inlined]
[16] #add_or_develop at .\none:0 [inlined]
[17] #add_or_develop#13 at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\Pkg\src\API.jl:29 [inlined]
[18] #add_or_develop at .\none:0 [inlined]
[19] #add_or_develop#12 at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\Pkg\src\API.jl:28 [inlined]
[20] #add_or_develop at .\none:0 [inlined]
[21] #add#20 at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\Pkg\src\API.jl:59 [inlined]
[22] add(::String) at C:\Users\julia\AppData\Local\Julia-1.0.3\share\julia\stdlib\v1.0\Pkg\src\API.jl:59
[23] top-level scope at C:\JuliaPro-1.0.3.1.atom\packages\julia-client\script\boot_repl.jl:22
[24] include at .\boot.jl:317 [inlined]
[25] include_relative(::Module, ::String) at .\loading.jl:1044
[26] include(::Module, ::String) at .\sysimg.jl:29
[27] exec_options(::Base.JLOptions) at .\client.jl:266
[28] _start() at .\client.jl:425
in expression starting at C:\JuliaPro-1.0.3.1.atom\packages\julia-client\script\boot_repl.jl:1

It was working for a lot of time
Then I just left an empty folder /registries, and it exhibits the same behavior, it is working for minutes without actually doing anything

@nbakas
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nbakas commented Apr 17, 2019

OK, I deleted everything from the registry (using regedit) as well as any folder created by the installation, reinstalled Julia and everything is working now

@ghost
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ghost commented Oct 26, 2019

I am having the same problem but cannot fix it. I just re-installed Julia Pro and when I try to add a package I get
git-repo `https://pkg.juliacomputing.com//registry/JuliaPro` ERROR: GitError(Code:EMERGECONFLICT, Class:Checkout, 619 conflicts prevent checkout) #checkout_tree#46(::LibGit2.CheckoutOptions, ::typeof(LibGit2.checkout_tree), ::LibGit2.GitRepo, ::LibGit2.GitCommit) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:? ffmerge!(::LibGit2.GitRepo, ::LibGit2.GitAnnotated) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:? #merge!#89(::LibGit2.MergeOptions, ::LibGit2.CheckoutOptions, ::typeof(LibGit2.merge!), ::LibGit2.GitRepo, ::Array{LibGit2.GitAnnotated,1}, ::Bool) at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/LibGit2/src/merge.jl:234 #merge! at ./none:0 [inlined] #merge!#140(::String, ::String, ::Bool, ::LibGit2.MergeOptions, ::LibGit2.CheckoutOptions, ::typeof(LibGit2.merge!), ::LibGit2.GitRepo) at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/LibGit2/src/LibGit2.jl:784 #merge! at ./none:0 [inlined] update_registries(::Pkg.Types.Context, ::Array{Pkg.Types.RegistrySpec,1}) at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Pkg/src/Types.jl:1254 update_registries at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Pkg/src/Types.jl:1219 [inlined] #handle_repos_add!#61(::Bool, ::Nothing, ::typeof(Pkg.Types.handle_repos_add!), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Pkg/src/Types.jl:719 #handle_repos_add! at ./none:0 [inlined] #add_or_develop#17(::Symbol, ::Bool, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.add_or_develop), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Pkg/src/API.jl:47 #add_or_develop at ./none:0 [inlined] #add_or_develop#16 at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Pkg/src/API.jl:36 [inlined] #add_or_develop at ./none:0 [inlined] #add_or_develop#13 at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Pkg/src/API.jl:34 [inlined] #add_or_develop at ./none:0 [inlined] #add_or_develop#12(::Base.Iterators.Pairs{Symbol,Symbol,Tuple{Symbol},NamedTuple{(:mode,),Tuple{Symbol}}}, ::typeof(Pkg.API.add_or_develop), ::String) at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Pkg/src/API.jl:33 #add_or_develop at ./none:0 [inlined] #add#22 at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Pkg/src/API.jl:64 [inlined] add(::String) at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Pkg/src/API.jl:64 top-level scope at none:0 eval at ./boot.jl:330 [inlined] (::getfield(Distributed, Symbol("##162#164")){Module,Expr})() at ./task.jl:268

@KristofferC
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Did you try #1161 (comment)?

@theburdman
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I have the same issue. Deleting the registry folder does not work for me on MacOS Catalina so I am dead in the water.

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@StefanKarpinski @KristofferC @fredrikekre @nbakas @theburdman