# Persistently dirty registry .... case-insensitive file collision when cloning JuliaRegistries/General from GitHub

**URL:** <https://discourse.julialang.org/t/persistently-dirty-registry-case-insensitive-file-collision-when-cloning-juliaregistries-general-from-github/41577>\
**Category:** General Usage\
**Created:** [June 17, 2020, 7:06am UTC](https://discourse.julialang.org/t/persistently-dirty-registry-case-insensitive-file-collision-when-cloning-juliaregistries-general-from-github/41577 "2020-06-17T07:06:24Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![lyonsquark](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/lyonsquark/32/4483_2.png) [@lyonsquark](https://discourse.julialang.org/u/lyonsquark)\
**Post date:** [June 17, 2020, 7:06am UTC](https://discourse.julialang.org/t/persistently-dirty-registry-case-insensitive-file-collision-when-cloning-juliaregistries-general-from-github/41577/1 "2020-06-17T07:06:24Z")

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Many Pkg commands are giving me

```julia
 Warning: Some registries failed to update:
│ — `~/.julia/registries/General` — registry dirty

```

and `] update` does not work.

Looking at my `~/.julia/registries/General`, there are files in `s/SAMtools` that git thinks are modified. They remain modified even after a `git reset --hard`. I finally deleted the repository and `git clone`’ed it and got…

```julia
> git clone https://github.com/JuliaRegistries/General.git  
# ...
warning: the following paths have collided (e.g. case-sensitive paths
on a case-insensitive filesystem) and only one from the same
colliding group is in the working tree:

  'S/SAMTools/Compat.toml'
  'S/SAMtools/Compat.toml'
  'S/SAMTools/Deps.toml'
  'S/SAMtools/Deps.toml'
  'S/SAMTools/Package.toml'
  'S/SAMtools/Package.toml'
  'S/SAMTools/Versions.toml'
  'S/SAMtools/Versions.toml'

```

I think this is my problem. I’m running on a Mac (which has a case insensitive file system). I see that there’s a commit regarding SAMTools a few hours ago. I think that’s messed things up.

Is there something I can do to get past this or do I need to wait for the repository in GitHub to be fixed?

Thanks!

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<div class="post-metadata">

**Author:** ![lyonsquark](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/lyonsquark/32/4483_2.png) [@lyonsquark](https://discourse.julialang.org/u/lyonsquark)\
**Post date:** [June 17, 2020, 7:11am UTC](https://discourse.julialang.org/t/persistently-dirty-registry-case-insensitive-file-collision-when-cloning-juliaregistries-general-from-github/41577/2 "2020-06-17T07:11:27Z")

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This doesn’t look good…

 ![image](https://global.discourse-cdn.com/julialang/original/3X/9/2/92d6352411b702c82919237e8cd392c173bf360e.png)

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**Author:** ![tamasgal](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tamasgal/32/27946_2.png) [@tamasgal](https://discourse.julialang.org/u/tamasgal)\
**Post date:** [June 17, 2020, 7:27am UTC](https://discourse.julialang.org/t/persistently-dirty-registry-case-insensitive-file-collision-when-cloning-juliaregistries-general-from-github/41577/3 "2020-06-17T07:27:53Z")

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Ah wait, updated: macOS does not have a case insensitive file system **by default** until APFS. Case insensitiveness is awkward. I did not notice that the recent introduction of APFS has this by default, that’s really annoying.

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<div class="post-metadata">

**Author:** ![Jakob](https://avatars.discourse-cdn.com/v4/letter/j/71c47a/32.png) [@Jakob](https://discourse.julialang.org/u/Jakob)\
**Post date:** [June 17, 2020, 7:53am UTC](https://discourse.julialang.org/t/persistently-dirty-registry-case-insensitive-file-collision-when-cloning-juliaregistries-general-from-github/41577/4 "2020-06-17T07:53:58Z")

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I’m having the same issue on Windows right now:

```julia
(@v1.4) pkg> up
   Updating registry at `C:\Users\Jakob\.julia\registries\General`
┌ Warning: Some registries failed to update:
│ — `C:\Users\Jakob\.julia\registries\General` — registry dirty
└ @ Pkg.Types D:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.4\Pkg\src\Types.jl:1122
   Updating git-repo `https://github.com/JuliaGraphs/LightGraphs.jl.git`
   Updating `C:\Users\Jakob\.julia\environments\v1.4\Project.toml`
 [no changes]
   Updating `C:\Users\Jakob\.julia\environments\v1.4\Manifest.toml`
 [no changes]

```

Following [this](https://discourse.julialang.org/t/registry-dirty/17989/27) discussion, i removed the `.julia\registries` folder and ran `up`, which however did not seem to help as the registry remained dirty.

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<div class="post-metadata">

**Author:** ![fredrikekre](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/fredrikekre/32/1688_2.png) [@fredrikekre](https://discourse.julialang.org/u/fredrikekre)\
**Post date:** [June 17, 2020, 8:32am UTC](https://discourse.julialang.org/t/persistently-dirty-registry-case-insensitive-file-collision-when-cloning-juliaregistries-general-from-github/41577/5 "2020-06-17T08:32:42Z")

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[https://github.com/JuliaRegistries/General/pull/16341](https://github.com/JuliaRegistries/General/pull/16341) should not have slipped throught CI. Should be fixed now after I merged [https://github.com/JuliaRegistries/General/pull/16502](https://github.com/JuliaRegistries/General/pull/16502).

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<div class="post-metadata">

**Author:** ![Jakob](https://avatars.discourse-cdn.com/v4/letter/j/71c47a/32.png) [@Jakob](https://discourse.julialang.org/u/Jakob)\
**Post date:** [June 17, 2020, 8:46am UTC](https://discourse.julialang.org/t/persistently-dirty-registry-case-insensitive-file-collision-when-cloning-juliaregistries-general-from-github/41577/6 "2020-06-17T08:46:37Z")

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I deleted the registry, ran `up` and everything is fine again 🙂 thanks for the quick fix!

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<div class="post-metadata">

**Author:** ![lyonsquark](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/lyonsquark/32/4483_2.png) [@lyonsquark](https://discourse.julialang.org/u/lyonsquark)\
**Post date:** [June 17, 2020, 3:26pm UTC](https://discourse.julialang.org/t/persistently-dirty-registry-case-insensitive-file-collision-when-cloning-juliaregistries-general-from-github/41577/7 "2020-06-17T15:26:41Z")

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Works for me now too! Thanks for fixing this problem quickly!