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Unable to add unregistered packages on macOS Monterey #2788

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SamuelBadr opened this issue Oct 21, 2021 · 21 comments
Closed

Unable to add unregistered packages on macOS Monterey #2788

SamuelBadr opened this issue Oct 21, 2021 · 21 comments
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@SamuelBadr
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Hi,

I'm unable to add unregistered packages (registered ones work just fine).

Specifically to test this issue, I started Julia with a new depot (export JULIA_DEPOT_PATH=/Users/samuel/tmp) and the first time I try to add an unregistered package, I get the below output followed by Julia crashing.

(@v1.6) pkg> add https://github.com/JuliaLang/Example.jl
     Cloning git-repo `https://github.com/JuliaLang/Example.jl`

signal (10): Bus error: 10
in expression starting at none:0
jl_system_image_data at /Applications/Julia-1.6.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
Allocations: 2649 (Pool: 2640; Big: 9); GC: 0
zsh: bus error  julia

After restarting Julia, the result changes to

(@v1.6) pkg> add https://github.com/JuliaLang/Example.jl
ERROR: GitError(Code:ENOTFOUND, Class:Repository, could not find repository from '/Users/samuel/tmp/clones/15037770950778237535')
Stacktrace:
  [1] macro expansion
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/LibGit2/src/error.jl:110 [inlined]
  [2] LibGit2.GitRepo(path::String)
    @ LibGit2 /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/LibGit2/src/repository.jl:11
  [3] #ensure_clone#2
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/GitTools.jl:70 [inlined]
  [4] handle_repo_add!(ctx::Pkg.Types.Context, pkg::Pkg.Types.PackageSpec)
    @ Pkg.Types /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:640
  [5] handle_repos_add!(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.Types /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:707
  [6] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Iterators.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:184
  [7] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:80
  [8] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:78
  [9] do_cmd!(command::Pkg.REPLMode.Command, repl::REPL.LineEditREPL)
    @ Pkg.REPLMode /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/REPLMode/REPLMode.jl:408
 [10] do_cmd(repl::REPL.LineEditREPL, input::String; do_rethrow::Bool)
    @ Pkg.REPLMode /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/REPLMode/REPLMode.jl:386
 [11] do_cmd
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/REPLMode/REPLMode.jl:377 [inlined]
 [12] (::Pkg.REPLMode.var"#24#27"{REPL.LineEditREPL, REPL.LineEdit.Prompt})(s::REPL.LineEdit.MIState, buf::IOBuffer, ok::Bool)
    @ Pkg.REPLMode /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/REPLMode/REPLMode.jl:550
 [13] #invokelatest#2
    @ ./essentials.jl:708 [inlined]
 [14] invokelatest
    @ ./essentials.jl:706 [inlined]
 [15] run_interface(terminal::REPL.Terminals.TextTerminal, m::REPL.LineEdit.ModalInterface, s::REPL.LineEdit.MIState)
    @ REPL.LineEdit /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/REPL/src/LineEdit.jl:2441
 [16] run_frontend(repl::REPL.LineEditREPL, backend::REPL.REPLBackendRef)
    @ REPL /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/REPL/src/REPL.jl:1126
 [17] (::REPL.var"#44#49"{REPL.LineEditREPL, REPL.REPLBackendRef})()
    @ REPL ./task.jl:411

and Julia no longer crashes. The same thing happens on master.

julia> versioninfo()
Julia Version 1.6.3
Commit ae8452a9e0 (2021-09-23 17:34 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin19.5.0)
  CPU: Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, skylake)
Environment:
  JULIA_NUM_THREADS = 6
  JULIA_DEPOT_PATH = /Users/samuel/tmp

Note that I'm on the current dev beta of macOS Monterey (21A558).

@staticfloat
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If you use a non-beta version of macOS Monterey, does it still occur?

Are there files in /Users/samuel/tmp/clones/15037770950778237535? If you run git fetch -C /Users/samuel/tmp/clones/15037770950778237535, what does it say?

@SamuelBadr
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There is no non-beta version of Monterey (At least until October 25, when the final releases. I'm on the RC).

~                                                                                                  
❯ ls -al ~/tmp/clones/15037770950778237535
total 0
drwxr-xr-x  2 samuel  staff  64 Oct 21 20:41 .
drwxr-xr-x  3 samuel  staff  96 Oct 21 20:41 ..

~                                                                                                  
❯ git fetch -C ~/tmp/clones/15037770950778237535
fatal: not a git repository (or any of the parent directories): .git

@staticfloat
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There is no non-beta version of Monterey (At least until October 25, when the final releases. I'm on the RC).

Indeed. :) I meant if you have access to a previous non-beta version on the same machine. But it's okay if you don't, we'll do our best to debug it nevertheless.

Okay, so the directory is just empty. My guess is that something is going badly wrong during initial clone, and then we don't clean up state properly. That signal (10): Bus error looks mighty suspicious; is it possible for you to run inside of lldb and get a backtrace? First, check to make sure that the following gives you the SIGBUS as well:

# Create new temporary depot, guaranteed to be empty
export JULIA_DEPOT_PATH=$(mktemp -d)

# This should error out
julia -e 'import Pkg; Pkg.add(url="https://github.com/JuliaLang/Example.jl")'

# Clean up depot path
rm -rf "${JULIA_DEPOT_PATH}"

If it does error out in the same way, then running inside of lldb and getting a backtrace may give us better insight into what exactly is going wrong:

export JULIA_DEPOT_PATH=$(mktemp -d)
lldb --args julia -e 'import Pkg; Pkg.add(url="https://github.com/JuliaLang/Example.jl")'

Once you get the (lldb) prompt, use r to run the program, then when it crashes, use bt to give a backtrace, and paste the full backtrace here.

@SamuelBadr
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I meant if you have access to a previous non-beta version on the same machine.

Oops seems obvious in hindsight! I don't, unfortunately, though :/

But it's okay if you don't, we'll do our best to debug it nevertheless.

Great, thank you!

So, after modifying your command slightly, this is what I got:

~                                                                                                  
❯ export JULIA_DEPOT_PATH=$(mktemp -d)

~                                                                                                  
❯ lldb -- /Applications/Julia-1.6.app/Contents/Resources/julia/bin/julia -e 'import Pkg; Pkg.add(url="https://github.com/JuliaLang/Example.jl")'
(lldb) target create "/Applications/Julia-1.6.app/Contents/Resources/julia/bin/julia"
Current executable set to '/Applications/Julia-1.6.app/Contents/Resources/julia/bin/julia' (x86_64).
(lldb) settings set -- target.run-args  "-e" "import Pkg; Pkg.add(url=\"https://github.com/JuliaLang/Example.jl\")"
(lldb) process launch
Process 70484 launched: '/Applications/Julia-1.6.app/Contents/Resources/julia/bin/julia' (x86_64)
     Cloning git-repo `https://github.com/JuliaLang/Example.jl`
Process 70484 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=2, address=0x113b09000)
    frame #0: 0x0000000113b09000 sys.dylib`jl_system_image_data + 142464
sys.dylib`jl_system_image_data:
->  0x113b09000 <+142464>: addb   %al, (%rax)
    0x113b09002 <+142466>: addb   %al, (%rax)
    0x113b09004 <+142468>: addb   %al, (%rax)
    0x113b09006 <+142470>: addb   %al, (%rax)
Target 0: (julia) stopped.
(lldb) bt
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=2, address=0x113b09000)
  * frame #0: 0x0000000113b09000 sys.dylib`jl_system_image_data + 142464
    frame #1: 0x000000011231f7a2 libgit2.1.3.0.dylib`git__clone + 252
    frame #2: 0x0000000112fb9f6f sys.dylib`julia_clone_54590.clone_1 at error.jl:108
    frame #3: 0x00000001138a9516 sys.dylib`julia_YY.cloneYY.122_54482.clone_1.clone_2 at LibGit2.jl:583
    frame #4: 0x00000001138a79e7 sys.dylib`julia_YY.cloneYY.3_51986.clone_1.clone_2 at LibGit2.jl:562
    frame #5: 0x000000011388b3e3 sys.dylib`julia_handle_repo_addNOT._48558.clone_1.clone_2 at GitTools.jl:87
    frame #6: 0x0000000113550b03 sys.dylib`japi1_handle_repos_addNOT._48741.clone_1.clone_2 at Types.jl:707
    frame #7: 0x000000011368895d sys.dylib`julia_YY.addYY.95_50233.clone_1.clone_2 at API.jl:184
    frame #8: 0x0000000113183e93 sys.dylib`julia_addYY.YY.kw_50111.clone_1 at API.jl:155
    frame #9: 0x0000000113183f00 sys.dylib`jfptr_addYY.YY.kw_50112.clone_1 + 80
    frame #10: 0x0000000101ce0fc0 libjulia-internal.1.6.dylib`jl_apply_generic + 1920
    frame #11: 0x00000001131d6990 sys.dylib`japi1_YY.addYY.24_50664.clone_1 at API.jl:80
    frame #12: 0x0000000101ce0fc0 libjulia-internal.1.6.dylib`jl_apply_generic + 1920
    frame #13: 0x0000000113169025 sys.dylib`japi1_add_50766.clone_1 at API.jl:78
    frame #14: 0x0000000111b13608
    frame #15: 0x0000000111b13742
    frame #16: 0x0000000101cf8260 libjulia-internal.1.6.dylib`do_call + 208
    frame #17: 0x0000000101cf6b95 libjulia-internal.1.6.dylib`eval_body + 1333
    frame #18: 0x0000000101cf6f0d libjulia-internal.1.6.dylib`jl_interpret_toplevel_thunk + 269
    frame #19: 0x0000000101d11845 libjulia-internal.1.6.dylib`jl_toplevel_eval_flex + 6165
    frame #20: 0x0000000101d11605 libjulia-internal.1.6.dylib`jl_toplevel_eval_flex + 5589
    frame #21: 0x0000000101d11605 libjulia-internal.1.6.dylib`jl_toplevel_eval_flex + 5589
    frame #22: 0x0000000101d12135 libjulia-internal.1.6.dylib`jl_toplevel_eval_in + 149
    frame #23: 0x000000011354d46c sys.dylib`julia_exec_options_39185.clone_1.clone_2 at boot.jl:360
    frame #24: 0x0000000112f8551b sys.dylib`julia__start_31087.clone_1 at client.jl:485
    frame #25: 0x0000000112f85676 sys.dylib`jfptr__start_31088.clone_1 + 6
    frame #26: 0x0000000101ce0fc0 libjulia-internal.1.6.dylib`jl_apply_generic + 1920
    frame #27: 0x0000000101d31133 libjulia-internal.1.6.dylib`true_main + 179
    frame #28: 0x0000000101d31024 libjulia-internal.1.6.dylib`repl_entrypoint + 164
    frame #29: 0x0000000100000f79 julia`main + 9
    frame #30: 0x000000010000c4fe dyld`start + 462
(lldb) 

Doesn't tell me anything tbh, but I'm hoping it's helpful?

@gbaraldi
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Can't reproduce the error or 1.7 on release Monterrey, tho I got some curl errors that didn't seem to affect it.

(@v1.7) pkg> add https://github.com/JuliaLang/Example.jl
     Cloning git-repo `https://github.com/JuliaLang/Example.jl`
    Updating git-repo `https://github.com/JuliaLang/Example.jl`
    Updating registry at `~/.julia/registries/General.toml`
┌ Error: curl_easy_setopt: 48
└ @ Downloads.Curl /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/Downloads/src/Curl/utils.jl:36
┌ Error: curl_easy_setopt: 48
└ @ Downloads.Curl /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/Downloads/src/Curl/utils.jl:36
┌ Error: curl_easy_setopt: 48
└ @ Downloads.Curl /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/Downloads/src/Curl/utils.jl:36
┌ Error: curl_easy_setopt: 48
└ @ Downloads.Curl /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/Downloads/src/Curl/utils.jl:36
┌ Error: curl_easy_setopt: 48
└ @ Downloads.Curl /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/Downloads/src/Curl/utils.jl:36
┌ Error: curl_easy_setopt: 48
└ @ Downloads.Curl /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/Downloads/src/Curl/utils.jl:36
   Resolving package versions...
    Updating `~/.julia/environments/v1.7/Project.toml`
  [7876af07] + Example v0.5.4 `https://github.com/JuliaLang/Example.jl#master`
    Updating `~/.julia/environments/v1.7/Manifest.toml`
  [7876af07] + Example v0.5.4 `https://github.com/JuliaLang/Example.jl#master`
Precompiling project...
  1 dependency successfully precompiled in 2 seconds (25 already precompiled)

@SamuelBadr
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Interesting data point! That means it's something with my particular config I guess.

As for the curl errors, see the Downloads.jl issue linked above; @staticfloat made a patch for that which will be in the 1.7 release build I believe.

@staticfloat
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What happens if you run:

julia> using LibGit2
       dir = mktempdir()
       LibGit2.clone("https://github.com/JuliaLang/Example.jl", dir)
LibGit2.GitRepo("/private/var/folders/0d/9vhfkswj7lb8smj9_p4hjnrh0000gn/T/jl_Ep3ZH0")

@SamuelBadr
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Same thing as before:

julia> using LibGit2

julia> dir = mktempdir()
"/var/folders/3d/g_t6f_0d6vjf31l8slt24lt00000gn/T/jl_8uTO19"

julia> LibGit2.clone("https://github.com/JuliaLang/Example.jl", dir)

signal (10): Bus error: 10
in expression starting at REPL[3]:1
jl_system_image_data at /Applications/Julia-1.6.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
Allocations: 2649 (Pool: 2640; Big: 9); GC: 0
zsh: bus error  julia

@DilumAluthge DilumAluthge changed the title Unable to add unregistered packages Unable to add unregistered packages on macOS Monterey Nov 1, 2021
@fredrikekre
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Maybe fixed by JuliaLang/julia#42721?

@SamuelBadr
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SamuelBadr commented Nov 8, 2021

I just tried on the nightly build and it still doesn't work, unfortunately.

EDIT: Ok, this is very interesting: While I get the same error message as before when I add https://github.com/JuliaLang/Example.jl, it appears to install it just fine (in contrast to 1.6.3). Like I can do using Example and use its functions etc.

@staticfloat
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When you start up the nightly, can you verify, using the dllist() function from the Libdl module, that no libraries are coming from /usr/local/?

@SamuelBadr
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~ ❯ julia-nightly
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.8.0-DEV.915 (2021-11-08)
 _/ |\__'_|_|_|\__'_|  |  Commit e3b9290e0c (0 days old master)
|__/                   |

julia> using Libdl

julia> any(lib -> occursin("/usr/local", lib), dllist())
false

@SamuelBadr
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SamuelBadr commented Nov 20, 2021

Just upgraded to 1.6.4 and this issue seems fixed.

Ok nvm :( With JuliaLang/Example.jl it works but e.g. https://github.com/longemen3000/BetterBanner.jl still doesn't.

@KristofferC
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Could you check #2788 (comment) again?

@SamuelBadr
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Sure! I tried on both 1.6.4 and the current master, but the result hasn't changed: There's no libraries loaded from /usr/local.

@KristofferC
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@staticfloat, any idea here?

@staticfloat
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No; I haven't been able to reproduce this error on any other machine, unfortunately. :(

@SamuelBadr
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I did a fresh install with 1.7 and it seems to work now! Thanks everybody!

@adamhsparks
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I see that this is closed, but I'm getting the same on macOS Monterey 1.7.1 as well now. I've done a fresh install to be sure.

julia> using Pkg

julia> add https://github.com/JuliaLang/Example.jl
ERROR: syntax: extra token "https" after end of expression
Stacktrace:
 [1] top-level scope
   @ none:1

Version info

Julia Version 1.7.1
Commit ac5cc99908 (2021-12-22 19:35 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin21.2.0)
  CPU: Apple M1
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-12.0.1 (ORCJIT, cyclone)

@SamuelBadr
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You need to enter Pkg mode by typing ] in the REPL, only then can you do add https://github.com/JuliaLang/Example.jl.

@adamhsparks
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OK, but that doesn't work either.

(@v1.7) pkg> add https://github.com/JuliaLang/Example.jl
ERROR: GitError(Code:ENOTFOUND, Class:Repository, could not find repository from '/Users/adamsparks/.julia/clones/15037770950778237535')
Stacktrace:
  [1] macro expansion
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/LibGit2/src/error.jl:110 [inlined]
  [2] LibGit2.GitRepo(path::String)
    @ LibGit2 /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/LibGit2/src/repository.jl:11
  [3] #ensure_clone#2
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/GitTools.jl:72 [inlined]
  [4] handle_repo_add!(ctx::Pkg.Types.Context, pkg::Pkg.Types.PackageSpec)
    @ Pkg.Types /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Types.jl:676
  [5] handle_repos_add!(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.Types /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Types.jl:743
  [6] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:248
  [7] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:149
  [8] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:144
  [9] do_cmd!(command::Pkg.REPLMode.Command, repl::REPL.LineEditREPL)
    @ Pkg.REPLMode /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/REPLMode/REPLMode.jl:407
 [10] do_cmd(repl::REPL.LineEditREPL, input::String; do_rethrow::Bool)
    @ Pkg.REPLMode /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/REPLMode/REPLMode.jl:385
 [11] do_cmd
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/REPLMode/REPLMode.jl:376 [inlined]
 [12] (::Pkg.REPLMode.var"#24#27"{REPL.LineEditREPL, REPL.LineEdit.Prompt})(s::REPL.LineEdit.MIState, buf::IOBuffer, ok::Bool)
    @ Pkg.REPLMode /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/REPLMode/REPLMode.jl:549
 [13] #invokelatest#2
    @ ./essentials.jl:716 [inlined]
 [14] invokelatest
    @ ./essentials.jl:714 [inlined]
 [15] run_interface(terminal::REPL.Terminals.TextTerminal, m::REPL.LineEdit.ModalInterface, s::REPL.LineEdit.MIState)
    @ REPL.LineEdit /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/LineEdit.jl:2493
 [16] run_frontend(repl::REPL.LineEditREPL, backend::REPL.REPLBackendRef)
    @ REPL /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/REPL/src/REPL.jl:1230
 [17] (::REPL.var"#49#54"{REPL.LineEditREPL, REPL.REPLBackendRef})()
    @ REPL ./task.jl:423

(@v1.7) pkg> 

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