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

Many Pkg commands are giving me

 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…

> git clone  
# ...
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:


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?


This doesn’t look good…

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.

1 Like

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

(@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 ``
   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 discussion, i removed the .julia\registries folder and ran up, which however did not seem to help as the registry remained dirty. should not have slipped throught CI. Should be fixed now after I merged


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

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