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 `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 discussion, i removed the .julia\registries folder and ran up, which however did not seem to help as the registry remained dirty.